bluuebunny/crossref_metadata_2025_split huggingface dataset:
Periodic switching of acoustic radiation force with beat created by multitone field
Authors: Tanaka Hiroya , Funayama Keita , Tadokoro Yukihiro 
Published: September 2022

AbstractAcoustic radiation force plays a key role in microfluidic systems for particle and cell manipulation. In this study, we investigate the acoustic radiation force resulting from synthesized ultrasounds that are emitted from multiple sound sources with slightly different oscillation frequencies. Due to the synthesized field, the acoustic radiation force is expressed as the sum of a dc component and harmonics of fundamental frequencies of a few hertz. This induces the beat of the acoustic radiation force. We demonstrate that the synthesized field provides the periodic on/off switching of the acoustic radiation force associated with the one denominational planar standing wave in a straight microfluidic channel. Consequently, our system can temporally manipulate acoustic radiation force without active controls.
Genome-wide association study of the human brain functional connectome reveals strong vascular component underlying global network efficiency
Authors: Bell Steven , Tozer Daniel J. , Markus Hugh S. 
Published: September 2022

AbstractComplex brain networks play a central role in integrating activity across the human brain, and such networks can be identified in the absence of any external stimulus. We performed 10 genome-wide association studies of resting state network measures of intrinsic brain activity in up to 36,150 participants of European ancestry in the UK Biobank. We found that the heritability of global network efficiency was largely explained by blood oxygen level-dependent (BOLD) resting state fluctuation amplitudes (RSFA), which are thought to reflect the vascular component of the BOLD signal. RSFA itself had a significant genetic component and we identified 24 genomic loci associated with RSFA, 157 genes whose predicted expression correlated with it, and 3 proteins in the dorsolateral prefrontal cortex and 4 in plasma. We observed correlations with cardiovascular traits, and single-cell RNA specificity analyses revealed enrichment of vascular related cells. Our analyses also revealed a potential role of lipid transport, store-operated calcium channel activity, and inositol 1,4,5-trisphosphate binding in resting-state BOLD fluctuations. We conclude that that the heritability of global network efficiency is largely explained by the vascular component of the BOLD response as ascertained by RSFA, which itself has a significant genetic component.
No evidence for carcinogenicity of titanium dioxide nanoparticles in 26-week inhalation study in rasH2 mouse model
Authors: Yamano Shotaro , Takeda Tomoki , Goto Yuko , Hirai Shigeyuki , Furukawa Yusuke , Kikuchi Yoshinori , Kasai Tatsuya , Misumi Kyohei , Suzuki Masaaki , Takanobu Kenji , Senoh Hideki , Saito Misae , Kondo Hitomi , Umeda Yumi 
Published: September 2022

AbstractWith the rapid development of alternative methods based on the spirit of animal welfare, the publications of animal studies evaluating endpoints such as cancer have been extremely reduced. We performed a 26-week inhalation exposure studies of titanium dioxide nanoparticles (TiO2 NPs) using CByB6F1-Tg(HRAS)2Jic (rasH2) mice model for detecting carcinogenicity. Male and female rasH2 mice were exposed to 2, 8 or 32 mg/m3 of TiO2 NPs for 6 h/day, 5 days/week for 26 weeks. All tissues and blood were collected and subjected to biological and histopathological analyses. TiO2 NPs exposure induced deposition of particles in lungs in a dose-dependent manner in each exposure group. Exposure to TiO2 NPs, as well as other organs, did not increase the incidence of lung tumors in any group, and pulmonary fibrosis and pre-neoplastic lesions were not observed in all groups. Finally, the cell proliferative activity of alveolar epithelial type 2 cells was examined, and it was not increased by exposure to TiO2 NPs. This is the first report showing the lack of pulmonary fibrogenicity and carcinogenicity (no evidence of carcinogenic activity) of TiO2 NPs in 26-week inhalation study in rasH2 mice exposed up to 32 mg/m3, which is considered to be a high concentration.
Importance of the Q/N-rich segment for protein stability of endogenous mouse TDP-43
Authors: Sato Toshiya , Oda Kanako , Sakai Seiko , Kato Rika , Yamamori Saori , Itakura Makoto , Kodera Yoshio , Nishizawa Masatoyo , Sasaoka Toshikuni , Onodera Osamu , Yokoyama Minesuke 
Published: September 2022

AbstractTAR DNA-binding protein 43 kDa (TDP-43), a nuclear protein, plays an important role in the molecular pathogenesis of amyotrophic lateral sclerosis (ALS). The long-disordered C-terminal region (CTR) of TDP-43 is known to be aggregation-prone and a hotspot for ALS mutations, so elucidation of the physiological function of CTR will provide insights into the pathogenesis of ALS. The CTR has two Gly, aromatic, and Ser-rich (GaroS) segments and an amyloidogenic core divided into a hydrophobic patch (HP) and a Gln/Asn (Q/N)-rich segment. Although TDP-43 lacking the CTR is known to be unstable, as observed in knock-in mice, it is unclear which of these segments contributes to the stability of TDP-43. Here, we generated 12 mouse lines lacking the various sub-regions of CTR by genome editing and compared the embryonic lethality of homozygotes, and protein and mRNA expression levels of TDP-43. We demonstrated the functional diversity of the four segments of CTR, finding that the presence of the Q/N-rich segment greatly restored the protein stability of TDP-43. In addition, we found that the second GaroS deletion did not affect protein stability and mouse development.
Robust mean shift filter for mixed Gaussian and impulsive noise reduction in color digital images
Authors: Kusnik Damian , Smolka Bogdan 
Published: September 2022

AbstractNoise reduction is one of the most important topics of digital image processing and despite the fact that it has been studied for a long time it remains the subject of active research. In the following work, we present an extension of the Mean Shift technique, which is efficiently reducing the Gaussian noise, so that it is able to cope with the impulsive disturbances. Furthermore, the elaborated technique can be applied to enhance the images corrupted by a mixture of strong Gaussian and impulsive noise, severely decreasing the quality of color digital images. By means of our approach, which is based on a novel similarity measure between a pixel and a patch located in the center of the processing block, even heavily disturbed images can be effectively restored, which enables the success of further stages of the image processing pipeline. We evaluate the efficiency of the proposed method using a publicly available database of test color images and compare the restored images applying a set of standard quality metrics with the results delivered by state-of-the-art denoising methods. Additionally, we compare our method with the Medoid and Quick Shift techniques, accelerating the original Mean Shift algorithm, in terms of objective quality criteria and computational complexity. The results of the performed experiments indicate that the proposed technique is superior to the widely used denoising techniques and can be used as a robust extension of the Mean Shift procedure. In the paper, a particular emphasis is placed on the ability of the presented algorithm to preserve and enhance image edges. The performed experiments evaluated with the use of the Pratt’s index, quantitatively confirm the superiority of the proposed design over the Mean Shift and standard denoising methods. The preservation of edges and even their sharpening is a very important feature of our algorithm whereas the final goal is segmentation, playing a crucial role in various computer vision tasks. The proposed algorithm is intended for the mixed noise reduction in color images, but it can be also applied in multispectral imaging and clustering of multidimensional data. To enable the comparison of our method with the standard denoising techniques and to help applying it in other image processing fields, we made its code freely available.
Cloud-enabled Biodepot workflow builder integrates image processing using Fiji with reproducible data analysis using Jupyter notebooks
Authors: Hung Ling-Hong , Straw Evan , Reddy Shishir , Schmitz Robert , Colburn Zachary , Yeung Ka Yee 
Published: September 2022

AbstractModern biomedical image analyses workflows contain multiple computational processing tasks giving rise to problems in reproducibility. In addition, image datasets can span both spatial and temporal dimensions, with additional channels for fluorescence and other data, resulting in datasets that are too large to be processed locally on a laptop. For omics analyses, software containers have been shown to enhance reproducibility, facilitate installation and provide access to scalable computational resources on the cloud. However, most image analyses contain steps that are graphical and interactive, features that are not supported by most omics execution engines. We present the containerized and cloud-enabled Biodepot-workflow-builder platform that supports graphics from software containers and has been extended for image analyses. We demonstrate the potential of our modular approach with multi-step workflows that incorporate the popular and open-source Fiji suite for image processing. One of our examples integrates fully interactive ImageJ macros with Jupyter notebooks. Our second example illustrates how the complicated cloud setup of an computationally intensive process such as stitching 3D digital pathology datasets using BigStitcher can be automated and simplified. In both examples, users can leverage a form-based graphical interface to execute multi-step workflows with a single click, using the provided sample data and preset input parameters. Alternatively, users can interactively modify the image processing steps in the workflow, apply the workflows to their own data, change the input parameters and macros. By providing interactive graphics support to software containers, our modular platform supports reproducible image analysis workflows, simplified access to cloud resources for analysis of large datasets, and integration across different applications such as Jupyter.
Changes in immunological parameters by ageing in rural healthy Indian adults and their associations with sex and lifestyle
Authors: Agarwal Dhiraj , Paul Sourav , Lele Pallavi , Piprode Vikrant , Kawade Anand , Hajela Neerja , Bavdekar Ashish , Parulekar Varsha , Ginde Manisha , Paranjape Gandhali , Matsuda Kazunori , Hori Tetsuji , Juvekar Sanjay , Lal Girdhari 
Published: September 2022

AbstractSeveral factors including sex and lifestyle have been reported to contribute to the age-related alteration of immune functions. The study was undertaken to determine age-related differences in the proportion of peripheral blood mononuclear lymphocytes in the Indian population using blood samples from 67 healthy adults (33 females and 34 males) aged between 20 and 80 years old. In the linear regression analysis to estimate the relationship with age categories, there was a significant increase in the frequency of natural killer cells with ageing, while their cytolytic activity significantly declined. The frequency of CD4+T cells increased with age, whereas that of CD8+T cells decreased, resulting in the age-associated increase of the CD4/CD8 ratio. The subsets of B cells did not show any significant relationship with age. Although there were variations between the male and female subgroups in effect size of ageing, the trends were in the same direction in all the parameters. Reduced fat intake was associated with a lower frequency of CD4+T cells, and higher serum cotinine level was associated with a higher CD4/CD8 ratio. The results indicate that cellular immunity in the Indian population is affected by ageing, while humoral immunity is less susceptible to ageing.
In silico analyses of Wnt1 nsSNPs reveal structurally destabilizing variants, altered interactions with Frizzled receptors and its deregulation in tumorigenesis
Authors: Mondal Amalesh , Paul Debarati , Dastidar Shubhra Ghosh , Saha Tanima , Goswami Achintya Mohan 
Published: September 2022

AbstractWnt1 is the first mammalian Wnt gene, which is discovered as proto-oncogene and in human the gene is located on the chromosome 12q13. Mutations in Wnt1 are reported to be associated with various cancers and other human diseases. The structural and functional consequences of most of the non-synonymous SNPs (nsSNPs), present in the human Wnt1 gene, are not known. In the present work, extensive bioinformatics analyses are used to screen 292 nsSNPs of Wnt1 for predicting pathogenic and harmless polymorphisms. We have identified 10 highly deleterious nsSNPs among which 7 are located within the highly conserved areas. These 10 nsSNPs are also predicted to affect the post-translational modifications of Wnt1. Further, structure based stability analyses of these 10 highly deleterious nsSNPs revealed 8 variants as highly destabilizing. These 8 highly destabilizing variants were shown to have high BC score and high RMSIP score from normal mode analyses. Based on the deformation energies, obtained from the normal mode analyses, variants like G169A, G169S, G331R and G331S were found to be unstable. Molecular Dynamics (MD) simulations revealed structural stability and fluctuation of WT Wnt1 and its prioritized variants. RMSD remained fluctuating mostly between 4 and 5 Å and occasionally between 3.5 and 5.5 Å ranges. RMSF in the CTD region (residues 330–360) of the binding pocket were lower compared to that of WT. Studying the impacts of nsSNPs on the binding interface of Wnt1 and seven Frizzled receptors have predicted substitutions which can stabilize or destabilize the binding interface. We have found that Wnt1 and FZD8-CRD is the best docked complex in our study. MD simulation based analyses of wild type Wnt1-FZD8-CRD complex and the 8 prioritized variants revealed that RMSF was higher in the unstructured regions and RMSD remained fluctuating in the region of 5 Å ± 1 Å. We have also observed differential Wnt1 gene expression pattern in normal, tumor and metastatic conditions across different tissues. Wnt1 gene expression was significantly higher in metastatic tissues of lungs, colon and skin; and was significantly lower in metastatic tissues of breast, esophagus and kidney. We have also found that Wnt1 deregulation is associated with survival outcome in patients with gastric and breast cancer. Furthermore, these computationally screened highly deleterious nsSNPs of Wnt1 can be analyzed in population based genetic studies and may help understand the Wnt1 associated diseases.
Drag reduction study of a microfiber-coated cylinder
Authors: Hasegawa Mitsugu , Chen Yi-Chung , Sakaue Hirotaka 
Published: September 2022

AbstractDrag reduction for a bluff body is imperative in a time of increasing awareness of the environmental impact and sustainability of air travel. Microfiber coating has demonstrated its ability to reduce drag on a bluff body. This was done by applying strips of the coating to a cylinder. To widen the application range of the microfiber coating, a fully microfiber-coated cylinder is studied as it has no directionality relative to incoming flow. It is hypothesized that a large coating coverage will cause a reduction in drag dependent on the Reynolds numberRe. The fully microfiber-coated cylinder is studied in a wind tunnel and the drag coefficient is determined at a range ofRein the subcritical-flow regime. It is found that the drag coefficient of the microfiber-coated cylinder is a function ofRe, and the critical Reynolds number, where the maximum drag reduction occurs, is lower for a microfiber-coated cylinder compared to that of a conventional smooth-surface cylinder.
Image copy-move forgery detection and localization based on super-BPD segmentation and DCNN
Authors: Li Qianwen , Wang Chengyou , Zhou Xiao , Qin Zhiliang 
Published: September 2022

AbstractWith the increasing importance of image information, image forgery seriously threatens the security of image content. Copy-move forgery detection (CMFD) is a greater challenge because its abnormality is smaller than other forgeries. To solve the problem that the detection results of the most image CMFD based on convolutional neural networks (CNN) have relatively low accuracy, an image copy-move forgery detection and localization based on super boundary-to-pixel direction (super-BPD) segmentation and deep CNN (DCNN) is proposed: SD-Net. Firstly, the segmentation technology is used to enhance the connection between the same or similar image blocks, improving the detection accuracy. Secondly, DCNN is used to extract image features, replacing conventional hand-crafted features with automatic learning features. The feature pyramid is used to improve the robustness to the scaling attack. Thirdly, the image BPD information is used to optimize the edges of rough detected image and obtain final detected image. The experiments proved that the SD-Net could detect and locate multiple, rotated, and scaling forgery well, especially large-level scaling forgery. Compared with other methods, the SD-Net is more accurately located and robust to various post-processing operations: brightness change, contrast adjustments, color reduction, image blurring, JPEG compression, and noise adding.
Analysis of solutions for a blockchain compliance with GDPR
Authors: Godyn Mateusz , Kedziora Michal , Ren Yingying , Liu Yongxin , Song Houbing Herbert 
Published: September 2022

AbstractThe aim of this paper was to perform an analysis of the state-of-the-art solutions of the permissioned blockchain compliance with the General Data Protection Regulation (GDPR), including the implementation of one of the analyzed methods and the own solution. This paper covers the subject of GDPR and its impact on already existing blockchain databases to determine the domain of the problem, including the necessity to introduce mutability in the data structure to comply with the ”right to be forgotten”. The performed analysis made it possible to discuss current research in technical terms as well as in the regulation itself. In the experimental part, attempts were made to research and implement the Reference-based Tree Structure (RBTS), including the performance tests. The proposed solution is efficient and easily reproducible. The deletion of unwanted content is quick and requires consent only from the owner of personal data; therefore, eliminating the dependency on the other blockchain network participants.
Effect of n-octanol on impurity removal by reverse flotation of magnesite ore
Authors: Li Pengcheng , Li Xiaoan , Dai Shujuan , Sun Wenhan , Zhou Bin 
Published: September 2022

AbstractDodecylamine is one of the most commonly used amine collectors for the reverse flotation of magnesite ore. Through a combination of experimental research and computational simulation, the effect of n-octanol on the removal of impurities by the reverse flotation of magnesite ore was studied. The test results show that when the dosage of dodecylamine was 60 mg/L, the flotation rates of magnesite and dolomite were 59.53% and 58.02%, respectively, and the flotation rate of quartz was 97.60%. In the presence of n-octanol, the flotation rate of magnesite decreased to 56.41%, and the flotation rates of dolomite and quartz increased to 61.30% and 99.59%, respectively. The test results show that the addition of n-octanol can improve the selectivity of minerals under the same amount of collector. The adsorption of dodecylamine (dodecylamine and n-octanol) on the surface of magnesite, dolomite and quartz was simulated using quantum chemical calculations based on density functional theory (DFT) and implemented in the CASTEP module of Materials Studio. The results show that dodecylamine can adsorb to magnesite, dolomite and quartz, and the adsorption effect was strongest on quartz. After adding n-octanol, the population value of the bond between the agent and magnesite decreased from 0.19 to 0.17, indicating that the adsorption effect of the agent on magnesite was weakened. The population value of the bond between the drug and dolomite increased from 0.19 to 0.23, indicating that the adsorption effect of the drug on dolomite was enhanced. H28, H29, and H2 in the drug form bonds with O12, O20, and O20 on the surface of quartz (101), respectively, and the population values were 0.43, 0.25, and 0.09, respectively. The adsorption sites of the drug and the quartz were increased, and the adsorption effect of the quartz was markedly improved. The test and simulation results show that the dosage of the agent can be reduced in the presence of n-octanol. N-octanol is not only beneficial to the removal of silicon by amine reverse flotation but also has a certain beneficial effect on the removal of calcium by reverse flotation.
Dynamics of phase oscillator networks with synaptic weight and structural plasticity
Authors: Chauhan Kanishk , Khaledi-Nasab Ali , Neiman Alexander B. , Tass Peter A. 
Published: September 2022

AbstractWe study the dynamics of Kuramoto oscillator networks with two distinct adaptation processes, one varying the coupling strengths and the other altering the network structure. Such systems model certain networks of oscillatory neurons where the neuronal dynamics, synaptic weights, and network structure interact with and shape each other. We model synaptic weight adaptation with spike-timing-dependent plasticity (STDP) that runs on a longer time scale than neuronal spiking. Structural changes that include addition and elimination of contacts occur at yet a longer time scale than the weight adaptations. First, we study the steady-state dynamics of Kuramoto networks that are bistable and can settle in synchronized or desynchronized states. To compare the impact of adding structural plasticity, we contrast the network with only STDP to one with a combination of STDP and structural plasticity. We show that the inclusion of structural plasticity optimizes the synchronized state of a network by allowing for synchronization with fewer links than a network with STDP alone. With non-identical units in the network, the addition of structural plasticity leads to the emergence of correlations between the oscillators’ natural frequencies and node degrees. In the desynchronized regime, the structural plasticity decreases the number of contacts, leading to a sparse network. In this way, adding structural plasticity strengthens both synchronized and desynchronized states of a network. Second, we use desynchronizing coordinated reset stimulation and synchronizing periodic stimulation to induce desynchronized and synchronized states, respectively. Our findings indicate that a network with a combination of STDP and structural plasticity may require stronger and longer stimulation to switch between the states than a network with STDP only.