bluuebunny/crossref_metadata_2025 huggingface dataset:
Remote Eye Gaze Tracking Research: A Comparative Evaluation on Past and Recent Progress
Authors: Shehu Ibrahim Shehi , Wang Yafei , Athuman Athuman Mohamed , Fu Xianping
Published: December 2021

Several decades of eye related research has shown how valuable eye gaze data are for applications that are essential to human daily life. Eye gaze data in a broad sense has been used in research and systems for eye movements, eye tracking, and eye gaze tracking. Since early 2000, eye gaze tracking systems have emerged as interactive gaze-based systems that could be remotely deployed and operated, known as remote eye gaze tracking (REGT) systems. The drop point of visual attention known as point of gaze (PoG), and the direction of visual attention known as line of sight (LoS), are important tasks of REGT systems. In this paper, we present a comparative evaluation of REGT systems intended for the PoG and LoS estimation tasks regarding past to recent progress. Our literature evaluation presents promising insights on key concepts and changes recorded over time in hardware setup, software process, application, and deployment of REGT systems. In addition, we present current issues in REGT research for future attempts.
Soft Robotic Sensing, Proprioception via Cable and Microfluidic Transmission
Authors: Lin Keng-Yu , Gamboa-Gonzalez Arturo , Wehner Michael
Published: December 2021

Current challenges in soft robotics include sensing and state awareness. Modern soft robotic systems require many more sensors than traditional robots to estimate pose and contact forces. Existing soft sensors include resistive, conductive, optical, and capacitive sensing, with each sensor requiring electronic circuitry and connection to a dedicated line to a data acquisition system, creating a rapidly increasing burden as the number of sensors increases. We demonstrate a network of fiber-based displacement sensors to measure robot state (bend, twist, elongation) and two microfluidic pressure sensors to measure overall and local pressures. These passive sensors transmit information from a soft robot to a nearby display assembly, where a digital camera records displacement and pressure data. We present a configuration in which one camera tracks 11 sensors consisting of nine fiber-based displacement sensors and two microfluidic pressure sensors, eliminating the need for an array of electronic sensors throughout the robot. Finally, we present a Cephalopod-chromatophore-inspired color cell pressure sensor. While these techniques can be used in a variety of soft robot devices, we present fiber and fluid sensing on an elastomeric finger. These techniques are widely suitable for state estimation in the soft robotics field and will allow future progress toward robust, low-cost, real-time control of soft robots. This increased state awareness is necessary for robots to interact with humans, potentially the greatest benefit of the emerging soft robotics field.
A 2.5-GS/s Four-Way-Interleaved Ringamp-Based Pipelined-SAR ADC with Digital Background Calibration in 28-nm CMOS
Authors: Lan Jingchao , Zhai Danfeng , Chen Yongzhen , Ni Zhekan , Shen Xingchen , Ye Fan , Ren Junyan
Published: December 2021

A 2.5-GS/s 12-bit four-way time-interleaved pipelined-SAR ADC is presented in 28-nm CMOS. A bias-enhanced ring amplifier is utilized as the residue amplifier to achieve high bandwidth and excellent power efficiency compared with a traditional operational amplifier. A high linearity front-end is proposed to alleviate the non-linearity of the diode for ESD protection in the input PAD. The embedded input buffer can suppress the kickback noise at high input frequencies. A blind background calibration based on digital-mixing is used to correct the mismatches between channels. Additionally, an optional neural network calibration is also provided. The prototype ADC achieves a low-frequency SNDR/SFDR of 51.0/68.0 dB, translating a competitive FoMw of 0.48 pJ/conv.-step at 250 MHz input running at 2.5 GS/s.
Memristive System Based Image Processing Technology: A Review and Perspective
Authors: Ji Xiaoyue , Dong Zhekang , Zhou Guangdong , Lai Chun Sing , Yan Yunfeng , Qi Donglian
Published: December 2021

As the acquisition, transmission, storage and conversion of images become more efficient, image data are increasing explosively. At the same time, the limitations of conventional computational processing systems based on the Von Neumann architecture continue to emerge, and thus, improving the efficiency of image processing has become a key issue that has bothered scholars working on images for a long time. Memristors with non-volatile, synapse-like, as well as integrated storage-and-computation properties can be used to build intelligent processing systems that are closer to the structure and function of biological brains. They are also of great significance when constructing new intelligent image processing systems with non-Von Neumann architecture and for achieving the integrated storage and computation of image data. Based on this, this paper analyses the mathematical models of memristors and discusses their applications in conventional image processing based on memristive systems as well as image processing based on memristive neural networks, to investigate the potential of memristive systems in image processing. In addition, recent advances and implications of memristive system-based image processing are presented comprehensively, and its development opportunities and challenges in different major areas are explored as well. By establishing a complete spectrum of image processing technologies based on memristive systems, this review attempts to provide a reference for future studies in the field, and it is hoped that scholars can promote its development through interdisciplinary academic exchanges and cooperation.
An Improved GWO Algorithm Optimized RVFL Model for Oil Layer Prediction
Authors: Lan Pu , Xia Kewen , Pan Yongke , Fan Shurui
Published: December 2021

In this study, a model based on the improved grey wolf optimizer (GWO) for optimizing RVFL is proposed to enable the problem of poor accuracy of Oil layer prediction due to the randomness of the parameters present in the random vector function link (RVFL) model to be addressed. Firstly, GWO is improved based on the advantages of chaos theory and the marine predator algorithm (MPA) to overcome the problem of low convergence accuracy in the optimization process of the GWO optimization algorithm. The improved GWO algorithm was then used to optimize the input weights and implicit layer biases of the RVFL network model so that the problem of inaccurate and unstable classification of RVFL due to the randomness of the parameters was avoided. MPA-GWO was used for comparison with algorithms of the same type under a function of 15 standard tests. From the results, it was concluded that it outperformed the algorithms of its type in terms of search accuracy and search speed. At the same time, the MPA-GWO-RVFL model was applied to the field of Oil layer prediction. From the comparison tests, it is concluded that the prediction accuracy of the MPA-GWO-RVFL model is on average 2.9%, 3.04%, 2.27%, 8.74%, 1.47% and 10.41% better than that of the MPA-RVFL, GWO-RVFL, PSO-RVFL, WOA-RVFL, GWFOA-RVFL and RVFL algorithms, respectively, and its practical applications are significant.
Net-Shape-Based Automated Detection of Integrated-Circuit Layout Plagiarism
Authors: Kasprowicz Dominik , Hayder Maria
Published: December 2021

Plagiarism of integrated-circuit (IC) layout is a problem encountered both in academia and in industry. A procedure was proposed that compares IC layouts based on the physical representation of particular electrical nets, i.e., on the shape of the features drawn on conducting layers (metals and polysilicon). At the heart of this method is the Needleman–Wunsch algorithm, used for decades in tools aligning sequences of amino acids or nucleotides. Here, it is used to quantify the visual similarity of nets within the pair of layouts being compared. The method was implemented in Python and successfully used to identify clusters of similar layouts within two pools of designs: one composed of logic gates and one containing operational transconductance amplifiers.
A Novel Progressive Image Classification Method Based on Hierarchical Convolutional Neural Networks
Authors: Li Cheng , Miao Fei , Gao Gang
Published: December 2021

Deep Neural Networks (DNNs) are commonly used methods in computational intelligence. Most prevalent DNN-based image classification methods are dedicated to promoting the performance by designing complicated network architectures and requiring large amounts of model parameters. These large-scale DNN-based models are performed on all images consistently. However, since there are meaningful differences between images, it is difficult to accurately classify all images by a consistent network architecture. For example, a deeper network is fit for the images that are difficult to be distinguished, but may lead to model overfitting for simple images. Therefore, we should selectively use different models to deal with different images, which is similar to the human cognition mechanism, in which different levels of neurons are activated according to the difficulty of object recognition. To this end, we propose a Hierarchical Convolutional Neural Network (HCNN) for image classification in this paper. HCNNs comprise multiple sub-networks, which can be viewed as different levels of neurons in humans, and these sub-networks are used to classify the images progressively. Specifically, we first initialize the weight of each image and each image category, and these images and initial weights are used for training the first sub-network. Then, according to the predicted results of the first sub-network, the weights of misclassified images are increased, while the weights of correctly classified images are decreased. Furthermore, the images with the updated weights are used for training the next sub-networks. Similar operations are performed on all sub-networks. In the test stage, each image passes through the sub-networks in turn. If the prediction confidences in a sub-network are higher than a given threshold, then the results are output directly. Otherwise, deeper visual features need to be learned successively by the subsequent sub-networks until a reliable image classification result is obtained or the last sub-network is reached. Experimental results show that HCNNs can obtain better results than classical CNNs and the existing models based on ensemble learning. HCNNs have 2.68% higher accuracy than Residual Network 50 (Resnet50) on the ultrasonic image dataset, 1.19% than Resnet50 on the chimpanzee facial image dataset, and 10.86% than Adaboost-CNN on the CIFAR-10 dataset. Furthermore, the HCNN is extensible, since the types of sub-networks and their combinations can be dynamically adjusted.
3D Visualization of Bamboo Node’s Vascular Bundle
Authors: Li Shan , Yang Shumin , Shang Lili , Liu Xinge , Ma Jianfeng , Ma Qianli , Tian Genlin
Published: December 2021

The vascular bundle is an important structural unit that determines the growth and properties of bamboo. A high-resolution X-ray microtomography (μCT) was used to observe and reconstruct a three-dimensional (3D) morphometry model of the vascular bundle of the Qiongzhuea tumidinoda node due to its advantages of quick, nondestructive, and accurate testing of plant internal structure. The results showed that the morphology of vascular bundles varied significantly in the axial direction. In the cross-section, the number of axial vascular bundles reached a maximum at the lower end of the sheath scar, and the minimum of it was at the middle of the diaphragm. The frequency of axial vascular bundles decreased from the lower end of the node to the nodal ridge, and subsequently increased until the upper end of the bamboo node. The proportion of parenchyma, fibers, and conducting tissue was 65.7%, 30.5%, and 3.8%, respectively. The conducting tissues were intertwined to form a complex 3D network structure, with a connectivity of 94.77%. The conducting tissue with the largest volume accounted for 60.26% of the total volume of the conducting tissue. The 3D-distribution pattern of the conducting tissue of the node and that of the fibers were similar, but their thickness changed in the opposite pattern. This study revealed the 3D morphometry of the conducting tissue and fibers of the bamboo node, the reconstruction of the skeleton made the morphology more intuitive. Quantitative indicators such as the 3D volume, proportion, and connectivity of each type of tissue was obtained, the bamboo node was enlarged mainly caused by the particularly developed fibers. This work laid the foundation for a better understanding of the mechanical properties and water transportation of bamboo and revealed the mystery of bamboo node shedding of Q. tumidinoda.
SilvAdapt.Net: A Site-Based Network of Adaptive Forest Management Related to Climate Change in Spain
Authors: Molina Antonio J. , Navarro-Cerrillo Rafael M. , Pérez-Romero Javier , Alejano Reyes , Bellot Juan F. , Blanco Juan A. , Camarero Jesús J. , Carrara Arnaud , Castillo Víctor M. , Cervera Teresa , Barberá Gonzalo G. , González-Sanchis María , Hernández Álvaro , Imbert Juan B. , Jiménez María N. , Llorens Pilar , Lucas-Borja Manuel E. , Moreno Gerardo , Heras Mariano Moreno-de las , Navarro Francisco B. , Palacios Guillermo , Palero Noemí , Ripoll María A. , Regües David , Ruiz-Gómez Francisco J. , Vilagrosa Alberto , del Campo Antonio D.
Published: December 2021

Adaptive forest management (AFM) is an urgent need because of the uncertainty regarding how changes in the climate will affect the structure, composition and function of forests during the next decades. Current research initiatives for the long-term monitoring of impacts of silviculture are scattered and not integrated into research networks, with the consequent losses of opportunities and capacity for action. To increase the scientific and practical impacts of these experiences, it is necessary to establish logical frameworks that harmonize the information and help us to define the most appropriate treatments. In this context, a number of research groups in Spain have produced research achievements and know-how during the last decades that can allow for the improvement in AFM. These groups address the issue of AFM from different fields, such as ecophysiology, ecohydrology and forest ecology, thus resulting in valuable but dispersed expertise. The main objective of this work is to introduce a comprehensive strategy aimed to study the implementation of AFM in Spain. As a first step, a network of 34 experimental sites managed by 14 different research groups is proposed and justified. As a second step, the most important AFM impacts on Mediterranean pines, as one of the most extended natural and planted forest types in Spain, are presented. Finally, open questions dealing with key aspects when attempting to implement an AFM framework are discussed. This study is expected to contribute to better outlining the procedures and steps needed to implement regional frameworks for AFM.
Effectiveness of Safety Interventions in Fire Engines to Reduce Potential Airborne Transmission of SARS-CoV-2
Authors: Bourdon Elmar , Schaefer Thomas , Kittel Maximilian , Raedle Matthias , Heininger Alexandra
Published: December 2021

Physical distancing and wearing a face mask are key interventions to prevent COVID-19. While this remains difficult to practice for millions of firefighters in fire engines responding to emergencies, the delayed forthcoming of evidence on the effectiveness of such safety interventions in this setting presents a major problem. In this field experimental study, we provided initial evidence to close this gap. We examined total aerosol burden in the cabin of a fire engine whilst manipulating crew size, use of FFP2 respirators and use of SCBA full-face masks during 15-min driving periods. At the same time, we controlled for crew activity and speaking, vehicle speed, cabin ventilation, cabin air temperature, pressure and humidity. Limiting the crew size, using FFP2 respirators and not donning SCBA full-face masks was associated with a reduction of the arithmetic mean of total aerosol burden of up to 49%. This study provided initial evidence on the effectiveness of safety interventions in fire engines to reduce potential airborne transmission of SARS-CoV-2 through aerosols. More research about the physical and the clinical effectiveness of such safety interventions is needed.
Swarm Intelligence Procedures Using Meyer Wavelets as a Neural Network for the Novel Fractional Order Pantograph Singular System
Authors: Sabir Zulqurnain , Raja Muhammad Asif Zahoor , Guirao Juan L. G. , Saeed Tareq
Published: December 2021

The purpose of the current investigation is to find the numerical solutions of the novel fractional order pantograph singular system (FOPSS) using the applications of Meyer wavelets as a neural network. The FOPSS is presented using the standard form of the Lane–Emden equation and the detailed discussions of the singularity, shape factor terms along with the fractional order forms. The numerical discussions of the FOPSS are described based on the fractional Meyer wavelets (FMWs) as a neural network (NN) with the optimization procedures of global/local search procedures of particle swarm optimization (PSO) and interior-point algorithm (IPA), i.e., FMWs-NN-PSOIPA. The FMWs-NN strength is pragmatic and forms a merit function based on the differential system and the initial conditions of the FOPSS. The merit function is optimized, using the integrated capability of PSOIPA. The perfection, verification and substantiation of the FOPSS using the FMWs is pragmatic for three cases through relative investigations from the true results in terms of stability and convergence. Additionally, the statics’ descriptions further authorize the presentation of the FMWs-NN-PSOIPA in terms of reliability and accuracy.
Spatial and Temporal Expression of High-Mobility-Group Nucleosome-Binding (HMGN) Genes in Brain Areas Associated with Cognition in Individuals with Down Syndrome
Authors: Rodríguez-Ortiz Alejandra , Montoya-Villegas Julio César , García-Vallejo Felipe , Mina-Paz Yecid
Published: December 2021

DNA methylation and histone posttranslational modifications are epigenetics processes that contribute to neurophenotype of Down Syndrome (DS). Previous reports present strong evidence that nonhistone high-mobility-group N proteins (HMGN) are epigenetic regulators. They play important functions in various process to maintain homeostasis in the brain. We aimed to analyze the differential expression of five human HMGN genes in some brain structures and age ranks from DS postmortem brain samples. Methodology: We performed a computational analysis of the expression of human HMGN from the data of a DNA microarray experiment (GEO database ID GSE59630). Using the transformed log2 data, we analyzed the differential expression of five HMGN genes in several brain areas associated with cognition in patients with DS. Moreover, using information from different genome databases, we explored the co-expression and protein interactions of HMNGs with the histones of nucleosome core particle and linker H1 histone. Results: We registered that HMGN1 and HMGN5 were significantly overexpressed in the hippocampus and areas of prefrontal cortex including DFC, OFC, and VFC of DS patients. Age-rank comparisons between euploid control and DS individuals showed that HMGN2 and HMGN4 were overexpressed in the DS brain at 16 to 22 gestation weeks. From the BioGRID database, we registered high interaction scores of HMGN2 and HMGN4 with Hist1H1A and Hist1H3A. Conclusions: Overall, our results give strong evidence to propose that DS would be an epigenetics-based aneuploidy. Remodeling brain chromatin by HMGN1 and HMGN5 would be an essential pathway in the modification of brain homeostasis in DS.
Lower Fractions of TCF4 Transcripts Spanning over the CTG18.1 Trinucleotide Repeat in Human Corneal Endothelium
Authors: Westin Ida Maria , Viberg Andreas , Byström Berit , Golovleva Irina
Published: December 2021

Fuchs’ endothelial corneal dystrophy (FECD) is a bilateral disease of the cornea caused by gradual loss of corneal endothelial cells. Late-onset FECD is strongly associated with the CTG18.1 trinucleotide repeat expansion in the Transcription Factor 4 gene (TCF4), which forms RNA nuclear foci in corneal endothelial cells. To date, 46 RefSeq transcripts of TCF4 are annotated by the National Center of Biotechnology information (NCBI), however the effect of the CTG18.1 expansion on expression of alternative TCF4 transcripts is not completely understood. To investigate this, we used droplet digital PCR for quantification of TCF4 transcripts spanning over the CTG18.1 and transcripts with transcription start sites immediately downstream of the CTG18.1. TCF4 expression was analysed in corneal endothelium and in whole blood of FECD patients with and without CTG18.1 expansion, in non-FECD controls without CTG18.1 expansion, and in five additional control tissues. Subtle changes in transcription levels in groups of TCF4 transcripts were detected. In corneal endothelium, we found a lower fraction of transcripts spanning over the CTG18.1 tract compared to all other tissues investigated.
Analysis of Peripheral Blood Mononuclear Cells Gene Expression Highlights the Role of Extracellular Vesicles in the Immune Response following Hematopoietic Stem Cell Transplantation in Children
Authors: Strojny Wojciech , Kwiecińska Kinga , Hałubiec Przemysław , Kowalczyk Wojciech , Miklusiak Karol , Łazarczyk Agnieszka , Skoczeń Szymon
Published: December 2021

Hematopoietic stem cell transplantation (HSCT) is an effective treatment method used in many neoplastic and non-neoplastic diseases that affect the bone marrow, blood cells, and immune system. The procedure is associated with a risk of adverse events, mostly related to the immune response after transplantation. The aim of our research was to identify genes, processes and cellular entities involved in the variety of changes occurring after allogeneic HSCT in children by performing a whole genome expression assessment together with pathway enrichment analysis. We conducted a prospective study of 27 patients (aged 1.5–18 years) qualified for allogenic HSCT. Blood samples were obtained before HSCT and 6 months after the procedure. Microarrays were used to analyze gene expressions in peripheral blood mononuclear cells. This was followed by Gene Ontology (GO) functional enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and protein–protein interaction (PPI) analysis using bioinformatic tools. We found 139 differentially expressed genes (DEGs) of which 91 were upregulated and 48 were downregulated. “Blood microparticle”, “extracellular exosome”, “B-cell receptor signaling pathway”, “complement activation” and “antigen binding” were among GO terms found to be significantly enriched. The PPI analysis identified 16 hub genes. Our results provide insight into a broad spectrum of epigenetic changes that occur after HSCT. In particular, they further highlight the importance of extracellular vesicles (exosomes and microparticles) in the post-HSCT immune response.
Transcriptomics View over the Germination Landscape in Biofortified Rice
Authors: Dueñas Conrado Jr. , Slamet-Loedin Inez , Macovei Anca
Published: December 2021

Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.
Single Cell Sequencing of Induced Pluripotent Stem Cell Derived Retinal Ganglion Cells (iPSC-RGC) Reveals Distinct Molecular Signatures and RGC Subtypes
Authors: Gudiseva Harini V. , Vrathasha Vrathasha , He Jie , Bungatavula Devesh , O’Brien Joan M. , Chavali Venkata R. M.
Published: December 2021

We intend to identify marker genes with differential gene expression (DEG) and RGC subtypes in cultures of human-induced pluripotent stem cell (iPSC)-derived retinal ganglion cells. Single-cell sequencing was performed on mature and functional iPSC-RGCs at day 40 using Chromium Single Cell 3’ V3 protocols (10X Genomics). Sequencing libraries were run on Illumina Novaseq to generate 150 PE reads. Demultiplexed FASTQ files were mapped to the hg38 reference genome using the STAR package, and cluster analyses were performed using a cell ranger and BBrowser2 software. QC analysis was performed by removing the reads corresponding to ribosomal and mitochondrial genes, as well as cells that had less than 1X mean absolute deviation (MAD), resulting in 4705 cells that were used for further analyses. Cells were separated into clusters based on the gene expression normalization via PCA and TSNE analyses using the Seurat tool and/or Louvain clustering when using BBrowser2 software. DEG analysis identified subsets of RGCs with markers like MAP2, RBPMS, TUJ1, BRN3A, SOX4, TUBB3, SNCG, PAX6 and NRN1 in iPSC-RGCs. Differential expression analysis between separate clusters identified significant DEG transcripts associated with cell cycle, neuron regulatory networks, protein kinases, calcium signaling, growth factor hormones, and homeobox transcription factors. Further cluster refinement identified RGC diversity and subtype specification within iPSC-RGCs. DEGs can be used as biomarkers for RGC subtype classification, which will allow screening model systems that represent a spectrum of diseases with RGC pathology.
Gene Amplification as a Mechanism of Yeast Adaptation to Nonsense Mutations in Release Factor Genes
Authors: Maksiutenko Evgeniia M. , Barbitoff Yury A. , Matveenko Andrew G. , Moskalenko Svetlana E. , Zhouravleva Galina A.
Published: December 2021

Protein synthesis (translation) is one of the fundamental processes occurring in the cells of living organisms. Translation can be divided into three key steps: initiation, elongation, and termination. In the yeast Saccharomyces cerevisiae, there are two translation termination factors, eRF1 and eRF3. These factors are encoded by the SUP45 and SUP35 genes, which are essential; deletion of any of them leads to the death of yeast cells. However, viable strains with nonsense mutations in both the SUP35 and SUP45 genes were previously obtained in several groups. The survival of such mutants clearly involves feedback control of premature stop codon readthrough; however, the exact molecular basis of such feedback control remain unclear. To investigate the genetic factors supporting the viability of these SUP35 and SUP45 nonsense mutants, we performed whole-genome sequencing of strains carrying mutant sup35-n and sup45-n alleles; while no common SNPs or indels were found in these genomes, we discovered a systematic increase in the copy number of the plasmids carrying mutant sup35-n and sup45-n alleles. We used the qPCR method which confirmed the differences in the relative number of SUP35 and SUP45 gene copies between strains carrying wild-type or mutant alleles of SUP35 and SUP45 genes. Moreover, we compare the number of copies of the SUP35 and SUP45 genes in strains carrying different nonsense mutant variants of these genes as a single chromosomal copy. qPCR results indicate that the number of mutant gene copies is increased compared to the wild-type control. In case of several sup45-n alleles, this was due to a disomy of the entire chromosome II, while for the sup35-218 mutation we observed a local duplication of a segment of chromosome IV containing the SUP35 gene. Taken together, our results indicate that gene amplification is a common mechanism of adaptation to nonsense mutations in release factor genes in yeast.
Genome-Wide Association Study Candidate Genes on Mammary System-Related Teat-Shape Conformation Traits in Chinese Holstein Cattle
Authors: Nazar Mudasir , Lu Xubin , Abdalla Ismail Mohamed , Ullah Numan , Fan Yongliang , Chen Zhi , Arbab Abdelaziz Adam Idriss , Mao Yongjiang , Yang Zhangping
Published: December 2021

In the dairy industry, mammary system traits are economically important for dairy animals, and it is important to explain their fundamental genetic architecture in Holstein cattle. Good and stable mammary system-related teat traits are essential for producer profitability in animal fitness and in the safety of dairy production. In this study, we conducted a genome-wide association study on three traits—anterior teat position (ATP), posterior teat position (PTP), and front teat length (FTL)—in which the FarmCPU method was used for association analyses. Phenotypic data were collected from 1000 Chinese Holstein cattle, and the GeneSeek Genomic Profiler Bovine 100K single-nucleotide polymorphisms (SNP) chip was used for cattle genotyping data. After the quality control process, 984 individual cattle and 84,406 SNPs remained for GWAS work analysis. Nine SNPs were detected significantly associated with mammary-system-related teat traits after a Bonferroni correction (p < 5.92 × 10−7), and genes within a region of 200 kb upstream or downstream of these SNPs were performed bioinformatics analysis. A total of 36 gene ontology (GO) terms and 3 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were significantly enriched (p < 0.05), and these terms and pathways are mainly related to metabolic processes, immune response, and cellular and amino acid catabolic processes. Eleven genes including MMS22L, E2F8, CSRP3, CDH11, PEX26, HAL, TAMM41, HIVEP3, SBF2, MYO16 and STXBP6 were selected as candidate genes that might play roles in the teat traits of cows. These results identify SNPs and candidate genes that give helpful biological information for the genetic architecture of these teat traits, thus contributing to the dairy production, health, and genetic selection of Chinese Holstein cattle.
Formation of the Codon Degeneracy during Interdependent Development between Metabolism and Replication
Authors: Li Dirson Jian
Published: December 2021

Nirenberg’s genetic code chart shows a profound correspondence between codons and amino acids. The aim of this article is to try to explain the primordial formation of the codon degeneracy. It remains a puzzle how informative molecules arose from the supposed prebiotic random sequences. If introducing an initial driving force based on the relative stabilities of triplex base pairs, the prebiotic sequence evolution became innately nonrandom. Thus, the primordial assignment of the 64 codons to the 20 amino acids has been explained in detail according to base substitutions during the coevolution of tRNAs with aaRSs; meanwhile, the classification of aaRSs has also been explained.
Longitudinal Changes in Cortical Thickness in Adolescents with Autism Spectrum Disorder and Their Association with Restricted and Repetitive Behaviors
Authors: Bieneck Valentina , Bletsch Anke , Mann Caroline , Schäfer Tim , Seelemeyer Hanna , Herøy Njål , Zimmermann Jennifer , Pretzsch Charlotte Marie , Hattingen Elke , Ecker Christine
Published: December 2021

The neuroanatomy of autism spectrum disorder (ASD) shows highly heterogeneous developmental trajectories across individuals. Mapping atypical brain development onto clinical phenotypes, and establishing their molecular underpinnings, is therefore crucial for patient stratification and subtyping. In this longitudinal study we examined intra- and inter-individual differences in the developmental trajectory of cortical thickness (CT) in childhood and adolescence, and their genomic underpinnings, in 33 individuals with ASD and 37 typically developing controls (aged 11–18 years). Moreover, we aimed to link regional atypical CT development to intra-individual variations in restricted and repetitive behavior (RRB) over a two-year time period. Individuals with ASD showed significantly reduced cortical thinning in several of the brain regions functionally related to wider autism symptoms and traits (e.g., fronto-temporal and cingulate cortices). The spatial patterns of the neuroanatomical differences in CT were enriched for genes known to be associated with ASD at a genetic and transcriptomic level. Further, intra-individual differences in CT correlated with within-subject variability in the severity of RRBs. Our findings represent an important step towards characterizing the neuroanatomical underpinnings of ASD across development based upon measures of CT. Moreover, our findings provide important novel insights into the link between microscopic and macroscopic pathology in ASD, as well as their relationship with different clinical ASD phenotypes.
Gene Flow and Genetic Structure Reveal Reduced Diversity between Generations of a Tropical Tree, Manilkara multifida Penn., in Atlantic Forest Fragments
Authors: Waqar Zubaria , Moraes Ramiris César Souza , Benchimol Maíra , Morante-Filho José Carlos , Mariano-Neto Eduardo , Gaiotto Fernanda Amato
Published: December 2021

The Atlantic Forest remnants in southern Bahia, Brazil, contain large tree species that have suffered disturbances in recent decades. Anthropogenic activities have led to a decrease in the population of many tree species and a loss of alleles that can maintain the evolutionary fitness of their populations. This study assessed patterns of genetic diversity, spatial genetic structure, and genetic structure among Manilkara multifida Penn. populations, comparing the genetic parameters of adult and juvenile trees. In particular, we collected leaves from adults and juveniles of M. multifida in two protected areas, the Veracel Station (EVC) and the Una Biological Reserve (UBR), located in threatened Atlantic Forest fragments. We observed a substantial decay in genetic variability between generations in both areas i.e., adults’ HO values were higher (EVC = 0.720, UBR = 0.736) than juveniles’ (EVC = 0.463 and UBR = 0.560). Both juveniles and adults showed genetic structure between the two areas (θ = 0.017 for adults and θ = 0.109 for juveniles). Additionally, forest fragments indicated an unexpectedly short gene flow. Our results, therefore, highlight the pervasive effects of historical deforestation and other human disturbances on the genetic diversity of M. multifida populations within a key conservation region of the Atlantic Forest biodiversity hotspot.
Carotenoid Biosynthetic Genes in Cabbage: Genome-Wide Identification, Evolution, and Expression Analysis
Authors: Cao Wenxue , Wang Peng , Yang Limei , Fang Zhiyuan , Zhang Yangyong , Zhuang Mu , Lv Honghao , Wang Yong , Ji Jialei
Published: December 2021

Carotenoids are natural functional pigments produced by plants and microorganisms and play essential roles in human health. Cabbage (Brassica oleracea L. var. capitata L.) is an economically important vegetable in terms of production and consumption. It is highly nutritious and contains β-carotene, lutein, and other antioxidant carotenoids. Here, we systematically analyzed carotenoid biosynthetic genes (CBGs) on the whole genome to understand the carotenoid biosynthetic pathway in cabbage. In total, 62 CBGs were identified in the cabbage genome, which are orthologs of 47 CBGs in Arabidopsis thaliana. Out of the 62 CBGs, 46 genes in cabbage were mapped to nine chromosomes. Evolutionary analysis of carotenoid biosynthetic orthologous gene pairs among B. oleracea, B. rapa, and A. thaliana revealed that orthologous genes of B. oleracea underwent a negative selection similar to that of B. rapa. Expression analysis of the CBGs showed functional differentiation of orthologous gene copies in B. oleracea and B. rapa. Exogenous phytohormone treatment suggested that ETH, ABA, and MeJA can promote some important CBGs expression in cabbage. Phylogenetic analysis showed that BoPSYs exhibit high conservatism. Subcellular localization analysis indicated that BoPSYs are located in the chloroplast. This study is the first to study carotenoid biosynthesis genes in cabbage and provides a basis for further research on carotenoid metabolic mechanisms in cabbage.
The Impact of COVID-19 Lockdowns on Satellite-Observed Aerosol Optical Thickness over the Surrounding Coastal Oceanic Areas of Megacities in the Coastal Zone
Authors: Wang Kai , Zhao Xuepeng
Published: December 2021

Nearly 40 years of aerosol optical thickness (AOT) climate data record (CDR) derived from NOAA operational satellite Advanced Very High Resolution Radiometer (AVHRR) observation over the global oceans is used to study the AOT changes due to the COVID-19 lockdown over the surrounding coastal oceanic areas of 18 megacities in the coast zone (MCCZ). The AOT difference between the annual mean AOT values of 2020 with COVID-19 lockdown and 2019 without the lockdown along with the 2020 AOT annual anomaly are used to effectively identify the AOT changes that are a result of the lockdown. We found that for most of the 18 MCCZ, the COVID-19 lockdowns implemented to contain the spread of the coronavirus resulted in a decrease between 1% and 30% in AOT due to reduced anthropogenic emissions associated with the lockdowns. However, the AOT long-term trend and other aerosol interannual variations due to favorable or unfavorable meteorological conditions may mask AOT changes due to the lockdown effect in some MCCZ. Different seasonal variations of aerosol amount in 2020 relative to 2019 due to other natural aerosol emission sources not influenced by the lockdown, such as dust storms and natural biomass burning and smoke, may also conceal a limited reduction in the annual mean AOT due to the lockdown in MCCZ with relatively loose lockdown. This study indicates that the use of long-term satellite observation is helpful for studying and monitoring the aerosol changes due to the emission reduction associated with the COVID-19 lockdown in the surrounding coastal oceanic areas of MCCZ, which will benefit the future development of the mitigation strategy for air pollution and emissions in megacities.
Effect of Base Conditions in One-Dimensional Numerical Simulation of Seismic Site Response: A Technical Note for Best Practice
Authors: Falcone Gaetano , Naso Giuseppe , Mori Federico , Mendicelli Amerigo , Acunzo Gianluca , Peronace Edoardo , Moscatelli Massimiliano
Published: December 2021

The effects induced by the choice of numerical base conditions for evaluating local seismic response are investigated in this technical note, aiming to provide guidelines for professional applications. A numerical modelling of the seismic site response is presented, assuming a one-dimensional scheme. At first, with reference to the case of a homogeneous soil layer overlying a half-space, two different types of numerical base conditions, named rigid and elastic, were adopted to analyse the seismic site response. Then, geological setting, physical and mechanical properties were selected from Italian case studies. In detail, the following stratigraphic successions were considered: shallow layer 1 (shear wave velocity, VS, equal to 400 m/s), layer 2 (VS equal to 600 m/s) and layer 3 (VS equal to 800 m/s). In addition, real signals were retrieved from the web site of the Italian accelerometric strong motion network. Rigid and elastic base conditions were adopted to estimate the ground motion modifications of the reference signals. The results are presented in terms of amplification factors (i.e., ratio of integral quantities referred to free-field and reference response spectra) and are compared between the adopted numerical models.
Integrated Assessment of Drought Impacts on Rural Areas: The Case of the Chapada Diamantina Region in Brazil
Authors: Ramos Ribeiro Rodrigo Rudge , Sulaiman Samia Nascimento , Sieber Stefan , Angel Trejo-Rangel Miguel , Campos Juliana Fionda
Published: December 2021

Drought is one of the most significant hazards that farmers face in rural areas. This study aims to examine an integrated assessment of the drought impacts in rural territories, considering the social perceptions related to the effects of natural hazards on health, social relations, income, and other impacts. The study area is located in the rural area of the Chapada Diamantina region in Northern Brazil. The characterization of the region was carried out based on historical meteorological and agricultural productivity data. The method used in this study was based on a survey of social perceptions regarding drought impacts by small rural producers through a participatory process. The results indicated how extreme events such as drought influence rural areas. In addition to agricultural productivity (~50%), aspects such as social migration and health problems were observed.
Fracture Spacing Variability and the Distribution of Fracture Patterns in Granitic Geothermal Reservoir: A Case Study in the Noble Hills Range (Death Valley, CA, USA)
Authors: Chabani Arezki , Trullenque Ghislain , Klee Johanne , Ledésert Béatrice A.
Published: December 2021

Scanlines constitute a robust method to better understand in 3D the fracture network variability in naturally fractured geothermal reservoirs. This study aims to characterize the spacing variability and the distribution of fracture patterns in a fracture granitic reservoir, and the impact of the major faults on fracture distribution and fluid circulation. The analogue target named the Noble Hills (NH) range is located in Death Valley (DV, USA). It is considered as an analogue of the geothermal reservoir presently exploited in the Upper Rhine Graben (Soultz-sous-Forêts, eastern of France). The methodology undertaken is based on the analyze of 10 scanlines located in the central part of the NH from fieldwork and virtual (photogrammetric models) data. Our main results reveal: (1) NE/SW, E/W, and NW/SE fracture sets are the most recorded orientations along the virtual scanlines; (2) spacing distribution within NH shows that the clustering depends on fracture orientation; and (3) a strong clustering of the fracture system was highlighted in the highly deformed zones and close to the Southern Death Valley fault zone (SDVFZ) and thrust faults. Furthermore, the fracture patterns were controlled by the structural heritage. Two major components should be considered in reservoir modeling: the deformation gradient and the proximity to the regional major faults.
Cultural Heritage and Rockfalls: Analysis of Multi-Scale Processes Nearby the Lucus Angitiae Archaeological Site (Central Italy)
Authors: Di Luzio Emiliano , Schilirò Luca , Gaudiosi Iolanda
Published: December 2021

Archaeological areas in the mountain region of central Italy can be seriously threatened by geological hazards, and efforts are required to preserve cultural heritage. The Lucus Angitiae is a pre-Roman site located along the western edge of the Fucino Basin, the largest continental depression of central Apennines. The carbonate slope overhanging the area is affected by active rockfall processes from two main rock escarpments. In this paper, rockfall assessment was pursued through a 3D kinematic modelling, performed by adopting a probabilistic approach. Specific attention was dedicated to the choice and calibration of the input data, based on field evidence and a literature review. Two different sizes of wedge-shaped rock blocks were identified on rock escarpments, and specific stability analyses were performed. Sensitivity analyses accounting for possible triggering factors, such as water pressure increase and seismic action, were also carried out, together with an investigation of the seismological characteristics of the area. The results of the numerical simulations were used to design effective countermeasures in the framework of a mitigation plan for protection of the archaeological site. Finally, clues of gravity-driven slope deformations at the slope scale were documented, framing the rockfall process in a wider geological scenario.
Effects of Governmental Intervention on Foodborne Disease Events: Evidence from China
Authors: Zhang Zhuang , Chen You-hua , Wu Lin-hai
Published: December 2021

Foodborne disease events (FDEs) endanger residents’ health around the world, including China. Most countries have formulated food safety regulation policies, but the effects of governmental intervention (GI) on FDEs are still unclear. So, this paper purposes to explore the effects of GI on FDEs by using Chinese provincial panel data from 2011 to 2019. The results show that: (i) GI has a significant negative impact on FDEs. Ceteris paribus, FDEs decreased by 1.3% when government expenditure on FDEs increased by 1%. (ii) By strengthening food safety standards and guiding enterprises to offer safer food, government can further improve FDEs. (iii) However, GI has a strong negative externality. Although GI alleviates FDEs in local areas, it aggravates FDEs in other areas. (iv) Compared with the eastern and coastal areas, the effects of GI on FDEs in the central, western, and inland areas are more significant. GI is conducive to ensuring Chinese health and equity. Policymakers should pay attention to two tasks in food safety regulation. Firstly, they should continue to strengthen GI in food safety issues, enhance food safety certification, and strive to ensure food safety. Secondly, they should reinforce the co-governance of regional food safety issues and reduce the negative externality of GI.
Attention to News Media, Emotional Responses, and Policy Preferences about Public Health Crisis: The Case of Fine Dust Pollution in South Korea
Authors: Kim Soohee , Kim Yong-Chan
Published: December 2021

This study examines how attention to science and political news may influence the way people feel about an environmental risk, and how this in turn impacts policy preferences. Using an online survey conducted on the issue of fine dust pollution in South Korea, this study found that science news attention was associated with greater anxiety and anger about the issue, whereas political news attention was associated with fear and sadness/depression (as well as anxiety and anger). Furthermore, mediation analysis showed that science news attention indirectly influenced support for preventive policy through anxiety, whereas political news attention indirectly influenced punitive policy support through anger and fear. Theoretical and practical implications of this study are discussed.