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Five different foam concretes were synthesized and examined. A new hybrid optical sensor, called combined digital holographic microscopy (CDHM), was proposed by combining microscopic fringe projection profilometry and lateral shearing digital holographic microscopy to detect the pore radii of produced foamed concretes. It was applied in addition to SEM and has not been applied to foam concretes before. Thanks to the proposed method, it was revealed that the measured CDHM radii contained a relative error of less than 6% compared to the SEM radii. The pore radii increased as the % of foaming agent used in the samples increased. Accordingly, the sample densities decreased and thermal insulation properties enhanced. Two-layer quantum chemical calculations performed at the ONIOM (M06-2X/6-31+G(d,p):UFF) theoretical level showed that thermodynamic stability of foam concretes increased as the % of foaming agent used, or more precisely, the pore radius, increased. The CDHM method provides results close to SEM and has superior features such as being more cost-effective, cleaner and faster. For this reason, it is thought that the proposed method will lead to future studies in terms of measuring pore radii as an alternative to SEM. Graphical Abstract The combined digital holographic microscopy (CDHM) method is proposed as an alternative to SEM with a relative error of less than 6% in determining the pore radius of foam concretes.

Background Zebrafish have practical features that make them a useful model for higher-throughput tests of gene function using CRISPR/Cas9 editing to create ‘knockout’ models. In particular, the use of G 0 mosaic mutants has potential to increase throughput of functional studies significantly but may suffer from transient effects of introducing Cas9 via microinjection. Further, a large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods leaving uncertainty in choosing an optimal approach for zebrafish studies. Methods To systematically assess accuracy of tool predictions of on- and off-target gene editing, we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs (gRNAs) targeting 14 genes. We also investigate potential confounders of G 0 -based CRISPR screens by assaying control embryos for spurious mutations and altered gene expression. Results We compared our experimental in vivo editing efficiencies in mosaic G 0 embryos with those predicted by eight commonly used gRNA design tools and found large discrepancies between methods. Assessing off-target mutations (predicted in silico and in vitro) found that the majority of tested loci had low in vivo frequencies (< 1%). To characterize if commonly used ‘mock’ CRISPR controls (larvae injected with Cas9 enzyme or mRNA with no gRNA) exhibited spurious molecular features that might exacerbate studies of G 0 mosaic CRISPR knockout fish, we generated an RNA-seq dataset of various control larvae at 5 days post fertilization. While we found no evidence of spontaneous somatic mutations of injected larvae, we did identify several hundred differentially-expressed genes with high variability between injection types. Network analyses of shared differentially-expressed genes in the ‘mock’ injected larvae implicated a number of key regulators of common metabolic pathways, and gene-ontology analysis revealed connections with response to wounding and cytoskeleton organization, highlighting a potentially lasting effect from the microinjection process that requires further investigation. Conclusion Overall, our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.

In this paper, a fuzzy interference and an adaptive neuro-fuzzy interference system models have been presented in order to accelerate designing of the digital holographic setup without experiment. The setting parameters of experimental holographic setup, which affect the quality of images obtained from reconstructed holograms, are predicted digitally by proposed models before the recording process. Hence, we reduce the required time for designing of digital holographic setup with optimization process. The adaptive neuro-fuzzy interference system model for the optimization of the digital holographic setup is first attempt in the literature. The accuracy of the proposed models is examined by comparing the presented models and actual calculated experimental root-mean-square values. As a result, the accuracy of the adaptive neuro-fuzzy interference system shows the better performance than the fuzzy interference system. Moreover, the design of experimental setup can be occurred numerically in a short time by using adaptive neuro-fuzzy interference system models.

The communication between the lines and contacts on the printed circuit boards (PCBs) is provided by the applied current flow. Due to thermal stress occurring in PCBs exposed to high currents, short-circuit faults (SCF) occur in PCB paths. During a quality PCB inspection before mass production, the initial occurrence time (IOT) of faults should be determined to intervene them at the earliest stage. PCBs are technological wastes that are difficult to recycle due to the diversity of material components and their difficulty of separation. By detecting the IOT of SCF at an early stage, the PCBs production can become recyclable without scrapping. Thus, the amount of PCB waste due to faulty production will be reduced. This paper proposes to diagnose the IOT of SCF that occur when currents (i.e., 8, 11.5, 13.5 Ampere) are applied to PCB paths. This process is performed using a hybrid optical imaging sensor (HOIS) in which lateral shearing digital holographic microscopy (LSDHM) is adapted to microscopic fringe projection profilometry (MFPP). In fault detection with MFPP, which is a surface detection method, the required illumination is provided by LSDHM. In thermal-based SCF diagnosis, a minimum of 36 seconds is required to reach the desired temperature (thermal saturation) for imaging while in optical inspection methods; additional time is required for the polarization process. In conventional methods, faults detection can be performed after only a visible PCB damage is occurred. In contrast, we detect the IOT of SCF in a short time of 1.1 seconds, eliminating the requirement of thermal saturation or polarization. Thanks to the HOIS, since faults are detected at an early stage, damage to the entire PCB will be prevented by repairing the faulty area before mass production.

World Health Organization has described the real-time reverse transcription-polymerase chain reaction test method for the diagnosis of the novel coronavirus disease (COVID-19). However, the limited number of test kits, the long-term results of the tests, the high probability of the disease spreading during the test and imaging without focused images necessitate the use of alternative diagnostic methods such as chest X-ray (CXR) imaging. The storage of data obtained for the diagnosis of the disease also poses a major problem. This causes misdiagnosis and delays treatment. In this work, we propose a hybrid 3D reconstruction method of CXR images (CXRI) to detect coronavirus pneumonia and prevent misdiagnosis on CXRI. We used the digital holography technique (DHT) for obtaining a priori information of CXRI stored in created digital hologram (CDH). In this way, the elimination of the storage problem that requires high space was revealed. In addition, Discrete Orthonormal S-Transform (DOST) is applied to the reconstructed CDH image obtained by using DHT. This method is called CDH_DHT_DOST. A multiresolution spatial-frequency representation of the lung images that belong to healthy people and diseased people with the COVID-19 virus is obtained by using the CDH_DHT_DOST. Moreover, the genetic algorithm (GA) is adopted for the reconstruction process for optimization of the CDH image and then DOST is applied. This hybrid method is called CDH_GA_DOST. Finally, we compare the results obtained from CDH_DHT_DOST and CDH_GA_DOST. The results show the feasibility of reconstructing CXRI with CDH_GA_DOST. The proposed method holds promises to meet demands for the detection of the COVID-19 virus. •Diagnosis of COVID-19 from chest X-ray image (CXRI) via digital holography (DH).•Created digital hologram (CDH) is used to store the CXRI.•Elimination of the storage problem that requires high space for CXRI with CDH.•Genetic algorithm (GA) and Discrete Orthonormal S-Transform (DOST) is used with DH.•A robust reconstructed CXRI is obtained via hybrid CDH_GA_DOST optimization method.

In recent years, zebrafish have become commonly used as a model for studying human traits and disorders. Their small size, high fecundity, and rapid development allow for more high-throughput experiments compared to other vertebrate models. Given that zebrafish share >70% gene homologs with humans and their genomes can be readily edited using highly efficient CRISPR methods, we are now able to rapidly generate mutations impacting practically any gene of interest. Unfortunately, our ability to phenotype mutant larvae has not kept pace. To address this challenge, we have developed a protocol that obtains multiple phenotypic measurements from individual zebrafish larvae in an automated and parallel fashion, including morphological features (i.e., body length, eye area, and head size) and movement/behavior. By assaying wild-type zebrafish in a variety of conditions, we determined optimal parameters that avoid significant developmental defects or physical damage; these include morphological imaging of larvae at two time points [3 days post fertilization (dpf) and 5 dpf] coupled with motion tracking of behavior at 5 dpf. As a proof-of-principle, we tested our approach on two novel CRISPR-generated mutant zebrafish lines carrying predicted null-alleles of syngap1b and slc7a5 , orthologs to two human genes implicated in autism-spectrum disorder, intellectual disability, and epilepsy. Using our optimized high-throughput phenotyping protocol, we recapitulated previously published results from mouse and zebrafish models of these candidate genes. In summary, we describe a rapid parallel pipeline to characterize morphological and behavioral features of individual larvae in a robust and consistent fashion, thereby improving our ability to better identify genes important in human traits and disorders.

The detection of crack on materials is an important issue in industry. On the contrary to conventional methods, such as manual inspection, sensor detection, and image processing techniques, a new simple method to detect the crack is proposed with optical voice recorder based on digital holography in this paper. Holograms obtained with sound waves passing through the materials are recorded by using the digital holography technique. Temporal behavior of the sound wave passing through the material, which is obtained from these holograms, gives image of crack. In this article, cracks in various materials are determined by the proposed new method, and crack images obtained with this new system are presented.

Zebrafish have practical features that make them a useful model for higher-throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. In particular, the use of G.sub.0 mosaic mutants has potential to increase throughput of functional studies significantly but may suffer from transient effects of introducing Cas9 via microinjection. Further, a large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods leaving uncertainty in choosing an optimal approach for zebrafish studies. To systematically assess accuracy of tool predictions of on- and off-target gene editing, we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs (gRNAs) targeting 14 genes. We also investigate potential confounders of G.sub.0-based CRISPR screens by assaying control embryos for spurious mutations and altered gene expression. We compared our experimental in vivo editing efficiencies in mosaic G.sub.0 embryos with those predicted by eight commonly used gRNA design tools and found large discrepancies between methods. Assessing off-target mutations (predicted in silico and in vitro) found that the majority of tested loci had low in vivo frequencies (< 1%). To characterize if commonly used 'mock' CRISPR controls (larvae injected with Cas9 enzyme or mRNA with no gRNA) exhibited spurious molecular features that might exacerbate studies of G.sub.0 mosaic CRISPR knockout fish, we generated an RNA-seq dataset of various control larvae at 5 days post fertilization. While we found no evidence of spontaneous somatic mutations of injected larvae, we did identify several hundred differentially-expressed genes with high variability between injection types. Network analyses of shared differentially-expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways, and gene-ontology analysis revealed connections with response to wounding and cytoskeleton organization, highlighting a potentially lasting effect from the microinjection process that requires further investigation. Overall, our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.

Hi-C characterizes three-dimensional chromatin organization, facilitates haplotype phasing, and enables genome-assembly scaffolding, but encounters difficulties across complex regions. By coupling chromosome conformation capture (3C) with PacBio HiFi long-read sequencing, here we develop a method (CiFi) that enables analysis of genomic interactions across repetitive regions. Starting with as little as 60,000 cells (sub-microgram DNA), the method produces multi-kilobasepair HiFi reads that contain multiple interacting, concatenated segments (~350 bp to 2 kbp). This multiplicity and increase in segment length versus standard short-read-based Hi-C improves read-mapping efficiency and coverage in repetitive regions and enhances haplotype phasing. CiFi pairwise interactions are largely concordant with Hi-C from a human lymphoblastoid cell line, with gains in assigning topologically associating domains across centromeres, segmental duplications, and human disease-associated genomic hotspots. As CiFi requires less input versus established methods, we apply the approach to characterize single small insects: assaying chromatin interactions across the genome from an Anopheles coluzzii mosquito and producing a chromosome-scale scaffolded assembly from a Ceratitis capitata Mediterranean fruit fly. Together, CiFi enables assessment of chromosome-scale interactions of previously recalcitrant low-complexity loci, low-input samples, and small organisms.

In this paper, the aim was to analyze in terms of noise the results of the methods used in reconstruction process of sound hologram obtained by optical voice recorder based on off-axis digital holography. In such a system, the sound holograms are captured by using human voice “a, e, i,” which is recorded in MP3 recorder and given to the medium by a loudspeaker. These sound holograms are obtained by using high-speed camera with the rate of 2000 frames per second and reconstructed by the commonly used methods (Fourier transform, Fresnel transform, and one-dimensional continuous wavelet transform methods) in the literature. In this study, the purpose is to compare and analyze the results obtained with these methods in terms of noise. This analysis is performed by giving the results obtained by the reconstruction process and by calculating the signal-to-noise ratio values with results obtained from the system.