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Wang, Weitao, Kyle N. Klein, Karel Proesmans, Hongbo Yang, Claire Marchal, Xiaopeng Zhu, Tyler Borrman i in. "Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication". Molecular Cell 81, nr 14 (lipiec 2021): 2975–88. http://dx.doi.org/10.1016/j.molcel.2021.05.024.
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Lacroix, Joris, Sandrine Pélofy, Charline Blatché, Marie-Jeanne Pillaire, Sébastien Huet, Catherine Chapuis, Jean-Sébastien Hoffmann i Aurélien Bancaud. "Analysis of DNA Replication by Optical Mapping in Nanochannels". Small 12, nr 43 (14.09.2016): 5963–70. http://dx.doi.org/10.1002/smll.201503795.
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Rhind, Nick, Weitao Wang, Kyle Klein, Karel Proesmans, Hongbo Yang, Alex Hastie, Feng Yue, John Bechhoefer, Chen Chunlong i David Gilbert. "Single‐Molecule Optical Replication Mapping (ORM) Suggests Human Replication Timing is Regulated by Stochastic Initiation". FASEB Journal 34, S1 (kwiecień 2020): 1. http://dx.doi.org/10.1096/fasebj.2020.34.s1.03352.
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Bayard, Quentin, Pierre Cordier, Camille Péneau, Sandrine Imbeaud, Theo Z. Hirsch, Victor Renault, Jean-Charles Nault i in. "Structure, Dynamics, and Impact of Replication Stress–Induced Structural Variants in Hepatocellular Carcinoma". Cancer Research 82, nr 8 (25.02.2022): 1470–81. http://dx.doi.org/10.1158/0008-5472.can-21-3665.
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Abstract Oncogene activation leads to replication stress and promotes genomic instability. Here we combine optical mapping and whole-genome sequencing (WGS) to explore in depth the nature of structural variants (SV) induced by replication stress in cyclin-activated hepatocellular carcinomas (CCN-HCC). In addition to classical tandem duplications, CCN-HCC displayed frequent intra-chromosomal and interchromosomal templated insertion cycles (TIC), likely resulting from template switching events. Template switching preferentially involves active topologically associated domains that are proximal to one another within the 3D genome. Template sizes depend on the type of cyclin activation and are coordinated within each TIC. Replication stress induced continuous accumulation of SVs during CCN-HCC progression, fostering the acquisition of new driver alterations and large-scale copy-number changes at TIC borders. Together, this analysis sheds light on the mechanisms, dynamics, and consequences of SV accumulation in tumors with oncogene-induced replication stress. Significance: Optical mapping and whole-genome sequencing integration unravels a unique signature of replication stress–induced structural variants that drive genomic evolution and the acquisition of driver events in CCN-HCC.
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Bayard, Quentin, Pierre Cordier, Camille Péneau, Sandrine Imbeaud, Theo Z. Hirsch, Victor Renault, Jean-Charles Nault i in. "Abstract LB545: Structure, dynamics and consequences of replication stress-induced structural variants in hepatocellular carcinoma". Cancer Research 82, nr 12_Supplement (15.06.2022): LB545. http://dx.doi.org/10.1158/1538-7445.am2022-lb545.
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Abstract Oncogene activation leads to replication stress and promotes genomic instability. Here we combine optical mapping and whole genome sequencing to explore in-depth the nature of structural variants (SVs) induced by replication stress in cyclin-activated hepatocellular carcinomas (CCN-HCC). In addition to classical tandem duplications, CCN-HCC display frequent intra- and inter-chromosomal templated insertion cycles (TIC) likely resulting from template switching events. Template switching preferentially involves active topologically associated domains that are close in the 3D genome organization. Template sizes depend on the type of cyclin activation and are coordinated within each TIC. Replication stress induces continuous accumulation of SVs during CCN-HCC progression, fostering the acquisition of new driver alterations and large-scale copy-number changes at TIC borders. Together, this analysis sheds light on the mechanisms, dynamics and consequences of SV accumulation in tumors with oncogene-induced replication stress. Citation Format: Quentin Bayard, Pierre Cordier, Camille Péneau, Sandrine Imbeaud, Theo Z. Hirsch, Victor Renault, Jean-Charles Nault, Jean-Frédéric Blanc, Julien Calderaro, Chantal Desdouets, Jessica Zucman-Rossi, Eric Letouzé. Structure, dynamics and consequences of replication stress-induced structural variants in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB545.
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Brewer, Bonita J., Maitreya J. Dunham i M. K. Raghuraman. "A unifying model that explains the origins of human inverted copy number variants". PLOS Genetics 20, nr 1 (4.01.2024): e1011091. http://dx.doi.org/10.1371/journal.pgen.1011091.
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With the release of the telomere-to-telomere human genome sequence and the availability of both long-read sequencing and optical genome mapping techniques, the identification of copy number variants (CNVs) and other structural variants is providing new insights into human genetic disease. Different mechanisms have been proposed to account for the novel junctions in these complex architectures, including aberrant forms of DNA replication, non-allelic homologous recombination, and various pathways that repair DNA breaks. Here, we have focused on a set of structural variants that include an inverted segment and propose that they share a common initiating event: an inverted triplication with long, unstable palindromic junctions. The secondary rearrangement of these palindromes gives rise to the various forms of inverted structural variants. We postulate that this same mechanism (ODIRA: origin-dependent inverted-repeat amplification) that creates the inverted CNVs in inherited syndromes also generates the palindromes found in cancers.
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De Carli, Francesco, Nikita Menezes, Wahiba Berrabah, Valérie Barbe, Auguste Genovesio i Olivier Hyrien. "High-Throughput Optical Mapping of Replicating DNA". Small Methods 2, nr 9 (6.08.2018): 1800146. http://dx.doi.org/10.1002/smtd.201800146.
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Atkinson, Noah, Tyler A. Morhart, Garth Wells, Grace T. Flaman, Eric Petro, Stuart Read, Scott M. Rosendahl, Ian J. Burgess i Sven Achenbach. "Microfabrication Process Development for a Polymer-Based Lab-on-Chip Concept Applied in Attenuated Total Reflection Fourier Transform Infrared Spectroelectrochemistry". Sensors 23, nr 14 (8.07.2023): 6251. http://dx.doi.org/10.3390/s23146251.
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Micro electro-mechanical systems (MEMS) combining sensing and microfluidics functionalities, as are common in Lab-on-Chip (LoC) devices, are increasingly based on polymers. Benefits of polymers include tunable material properties, the possibility of surface functionalization, compatibility with many micro and nano patterning techniques, and optical transparency. Often, additional materials, such as metals, ceramics, or silicon, are needed for functional or auxiliary purposes, e.g., as electrodes. Hybrid patterning and integration of material composites require an increasing range of fabrication approaches, which must often be newly developed or at least adapted and optimized. Here, a microfabrication process concept is developed that allows one to implement attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and electrochemistry on an LoC device. It is designed to spatially resolve chemical sensitivity and selectivity, which are instrumental for the detection of chemical distributions, e.g., during on-flow chemical and biological reaction chemistry. The processing sequence involves (i) direct-write and soft-contact UV lithography in SUEX dry resist and replication in polydimethylsiloxane (PDMS) elastomers as the fluidic structure; (ii) surface functionalization of PDMS with oxygen plasma, 3-aminopropyl-triethoxysilane (APTES), and a UV-curable glue (NOA 73) for bonding the fluidic structure to the substrate; (iii) double-sided patterning of silicon nitride-coated silicon wafers serving as the ATR-FTIR-active internal reflection element (IRE) on one side and the electrode-covered substrate for microfluidics on the back side with lift-off and sputter-based patterning of gold electrodes; and (iv) a custom-designed active vacuum positioning and alignment setup. Fluidic channels of 100 μm height and 600 μm width in 5 mm thick PDMS were fabricated on 2” and 4” demonstrators. Electrochemistry on-chip functionality was demonstrated by cyclic voltammetry (CV) of redox reactions involving iron cyanides in different oxidation states. Further, ATR-FTIR measurements of laminar co-flows of H2O and D2O demonstrated the chemical mapping capabilities of the modular fabrication concept of the LoC devices.
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Fearns, Rachel, Mark E. Peeples i Peter L. Collins. "Mapping the Transcription and Replication Promoters of Respiratory Syncytial Virus". Journal of Virology 76, nr 4 (15.02.2002): 1663–72. http://dx.doi.org/10.1128/jvi.76.4.1663-1672.2002.
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ABSTRACT An important, unresolved issue in mononegavirus biology is whether or not transcription is initiated by the same promoter as RNA replication. In this study, residues important for respiratory syncytial virus (RSV) transcription and RNA replication were identified by subjecting the first 26 nucleotides of genome RNA to saturation mutagenesis. This analysis was performed using a genome analog that allowed transcription and RNA replication to be dissociated from each other and monitored as independent events in an intracellular assay. This analysis showed that nucleotides 3C, 5C, 8U, 9U, 10U, and 11U were important for transcription and RNA replication. Additional nucleotides (1U, 2G, 6U, and 7U) were important for RNA replication, but not transcription. At position 4, G versus C or U augmented transcription and decreased replication, showing that the naturally occurring assignments in the genomic (4G) and antigenomic (4U) promoters are optimal for transcription and RNA replication, respectively. These data show that RSV transcription and RNA replication each involve a cis-acting signal at the very 3" end of the genome. This signal appears to contain a minimum, common element that functions in both transcription and RNA replication, defined by those substitutions that had similar effects on the two processes. Apart from these common nucleotides, other positions were involved in RNA replication but not transcription or had different effects on the two processes. This indicates that the promoters for transcription and replication involve overlapping sets of nucleotides at the very 3" end of the genome and provides evidence that the nucleotide preferences for the two processes are not identical.
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Sung, Yen-Ling, Yuan-Si Tsai, Chu-Ling Chang, Chih-Kuan Chen, Chih-Hua Wang i Yi-Chun Lin. "(Invited) Cardiac Engineering: Optical Mapping in Cellular Communication". ECS Meeting Abstracts MA2024-01, nr 33 (9.08.2024): 1652. http://dx.doi.org/10.1149/ma2024-01331652mtgabs.
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Microfluidic platforms have emerged as valuable tools for replicating the adverse effects of chemotherapy drugs on cardiac and non-cardiac cells in vitro. However, these systems currently fall short of comprehensively capturing the intricate nature of human responses to chemotherapy, necessitating further validation to enhance model accuracy. While innovative chip systems provide insightful means for screening cardiac toxicity, they encounter challenges in addressing individual variations in drug responses and the influence of patient-specific factors. A novel cardiac chip incorporating intracellular electrophysiological techniques was developed to monitor acute hypoxia-induced responses in cardiac cells. Despite its promising potential, the model exhibits limitations inherent to its simplified two-dimensional microfluidic system, warranting additional validation and optimization efforts to enhance physiological relevance and facilitate applications in clinical translation. Moreover, previous research has proposed the formation of functional connections between human neurons and myocardial cells in a microfluidic chip. However, this study primarily focused on one-way connections between neurons and myocardial cells, overlooking the complexities of bidirectional neuro-muscular connections. Consequently, further research is imperative to deepen our understanding of the intricate interactions between neurons and myocardial cells. Optical mapping techniques assessed transmembrane voltage, mitochondrial activity, and calcium signals during electric pacing. These comprehensive assessments aim to advance our understanding of cardiac electrophysiology under drug exposure, providing crucial insights into the intricate responses of cardiac cells to chemotherapy. This research has significant implications for enhancing our understanding of cardiac safety in the context of chemotherapy.
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Lambertini, Alessandro, Emanuele Mandanici, Maria Alessandra Tini i Luca Vittuari. "Technical Challenges for Multi-Temporal and Multi-Sensor Image Processing Surveyed by UAV for Mapping and Monitoring in Precision Agriculture". Remote Sensing 14, nr 19 (4.10.2022): 4954. http://dx.doi.org/10.3390/rs14194954.
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Precision Agriculture (PA) is an approach to maximizing crop productivity in a sustainable manner. PA requires up-to-date, accurate and georeferenced information on crops, which can be collected from different sensors from ground, aerial or satellite platforms. The use of optical and thermal sensors from Unmanned Aerial Vehicle (UAV) platform is an emerging solution for mapping and monitoring in PA, yet many technological challenges are still open. This technical note discusses the choice of UAV type and its scientific payload for surveying a sample area of 5 hectares, as well as the procedures for replicating the study on a larger scale. This case study is an ideal opportunity to test the best practices to combine the requirements of PA surveys with the limitations imposed by local UAV regulations. In the field area, to follow crop development at various stages, nine flights over a period of four months were planned and executed. The usage of ground control points for optimal georeferencing and accurate alignment of maps created by multi-temporal processing is analyzed. Output maps are produced in both visible and thermal bands, after appropriate strip alignment, mosaicking, sensor calibration, and processing with Structure from Motion techniques. The discussion of strategies, checklists, workflow, and processing is backed by data from more than 5000 optical and radiometric thermal images taken during five hours of flight time in nine flights throughout the crop season. The geomatics challenges of a georeferenced survey for PA using UAVs are the key focus of this technical note. Accurate maps derived from these multi-temporal and multi-sensor surveys feed Geographic Information Systems (GIS) and Decision Support Systems (DSS) to benefit PA in a multidisciplinary approach.
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Perez, Daniel R., i Ruben O. Donis. "Functional Analysis of PA Binding by Influenza A Virus PB1: Effects on Polymerase Activity and Viral Infectivity". Journal of Virology 75, nr 17 (1.09.2001): 8127–36. http://dx.doi.org/10.1128/jvi.75.17.8127-8136.2001.
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ABSTRACT Influenza A virus expresses three viral polymerase (P) subunits—PB1, PB2, and PA—all of which are essential for RNA and viral replication. The functions of P proteins in transcription and replication have been partially elucidated, yet some of these functions seem to be dependent on the formation of a heterotrimer for optimal viral RNA transcription and replication. Although it is conceivable that heterotrimer subunit interactions may allow a more efficient catalysis, direct evidence of their essentiality for viral replication is lacking. Biochemical studies addressing the molecular anatomy of the P complexes have revealed direct interactions between PB1 and PB2 as well as between PB1 and PA. Previous studies have shown that the N-terminal 48 amino acids of PB1, termed domain α, contain the residues required for binding PA. We report here the refined mapping of the amino acid sequences within this small region of PB1 that are indispensable for binding PA by deletion mutagenesis of PB1 in a two-hybrid assay. Subsequently, we used site-directed mutagenesis to identify the critical amino acid residues of PB1 for interaction with PA in vivo. The first 12 amino acids of PB1 were found to constitute the core of the interaction interface, thus narrowing the previous boundaries of domain α. The role of the minimal PB1 domain α in influenza virus gene expression and genome replication was subsequently analyzed by evaluating the activity of a set of PB1 mutants in a model reporter minigenome system. A strong correlation was observed between a functional PA binding site on PB1 and P activity. Influenza viruses bearing mutant PB1 genes were recovered using a plasmid-based influenza virus reverse genetics system. Interestingly, mutations that rendered PB1 unable to bind PA were either nonviable or severely growth impaired. These data are consistent with an essential role for the N terminus of PB1 in binding PA, P activity, and virus growth.
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Raseley, Kaitlin, Zeal Jinwala, Dong Zhang i Ming Xiao. "Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM) Can Potentially Define the ALT Positivity of Cancer". Genes 14, nr 6 (16.06.2023): 1278. http://dx.doi.org/10.3390/genes14061278.
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Telomeres play an essential role in protecting the ends of linear chromosomes and maintaining the integrity of the human genome. One of the key hallmarks of cancers is their replicative immortality. As many as 85–90% of cancers activate the expression of telomerase (TEL+) as the telomere maintenance mechanism (TMM), and 10–15% of cancers utilize the homology-dependent repair (HDR)-based Alternative Lengthening of Telomere (ALT+) pathway. Here, we performed statistical analysis of our previously reported telomere profiling results from Single Molecule Telomere Assay Optical Mapping (SMTA-OM), which is capable of quantifying individual telomeres from single molecules across all chromosomes. By comparing the telomeric features from SMTA-OM in TEL+ and ALT+ cancer cells, we demonstrated that ALT+ cancer cells display certain unique telomeric profiles, including increased fusions/internal telomere-like sequence (ITS+), fusions/internal telomere-like sequence loss (ITS−), telomere-free ends (TFE), super-long telomeres, and telomere length heterogeneity, compared to TEL+ cancer cells. Therefore, we propose that ALT+ cancer cells can be differentiated from TEL+ cancer cells using the SMTA-OM readouts as biomarkers. In addition, we observed variations in SMTA-OM readouts between different ALT+ cell lines that may potentially be used as biomarkers for discerning types of ALT+ cancer and monitoring cancer therapy.
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M, Abhinaya, i A. Umamakeswari. "A Robust Image Watermarking Method based on Contourlet Transform for Correcting Geometric Attacks". International Journal of Engineering & Technology 7, nr 2.24 (25.04.2018): 24. http://dx.doi.org/10.14419/ijet.v7i2.24.11992.
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A watermarking technique is proposed using Discrete Wavelet Transform (DWT), Discrete Cosine Transform (DCT), and Singular Value Decomposition (SVD) techniques to implement information hiding. Embedding can be done by dividing the host image into four rectangular segments which are non-overlapping called sub-images using hybrid scheme. Redundancy reduces cropping attack. The main aim is to reduce the effect of geometric bouts, such as rotation, translation, and affine translation using synchronization technique. Watermarks can be a binary random sequence of different lengths. Data replication and hamming code are two error modification methods utilized in the proposed scheme. Achieved results show comparable robustness against geometric attacks and signal processing. Contourlet transform can be used to improve the visual feature of the image. After embedding the image or data, contourlet transform is applied in the frequency domain to improve robustness. The optimal mapping function is obtained using contourlet transform which increases Peak Signal to Noise Ratio (PSNR) and hiding capacity with low distortion.
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Zuo, Pengcheng, Dong Ma, Qingbo Liu, Lizhong Jiang i Yang Chen. "Photonics-assisted microwave pulse detection and frequency measurement based on pulse replication and frequency-to-time mapping". Applied Optics 61, nr 7 (23.02.2022): 1639. http://dx.doi.org/10.1364/ao.450247.
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Ball, Heather L., Mark R. Ehrhardt, Daniel A. Mordes, Gloria G. Glick, Walter J. Chazin i David Cortez. "Function of a Conserved Checkpoint Recruitment Domain in ATRIP Proteins". Molecular and Cellular Biology 27, nr 9 (5.03.2007): 3367–77. http://dx.doi.org/10.1128/mcb.02238-06.
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ABSTRACT The ATR (ATM and Rad3-related) kinase is essential to maintain genomic integrity. ATR is recruited to DNA lesions in part through its association with ATR-interacting protein (ATRIP), which in turn interacts with the single-stranded DNA binding protein RPA (replication protein A). In this study, a conserved checkpoint protein recruitment domain (CRD) in ATRIP orthologs was identified by biochemical mapping of the RPA binding site in combination with nuclear magnetic resonance, mutagenesis, and computational modeling. Mutations in the CRD of the Saccharomyces cerevisiae ATRIP ortholog Ddc2 disrupt the Ddc2-RPA interaction, prevent proper localization of Ddc2 to DNA breaks, sensitize yeast to DNA-damaging agents, and partially compromise checkpoint signaling. These data demonstrate that the CRD is critical for localization and optimal DNA damage responses. However, the stimulation of ATR kinase activity by binding of topoisomerase binding protein 1 (TopBP1) to ATRIP-ATR can occur independently of the interaction of ATRIP with RPA. Our results support the idea of a multistep model for ATR activation that requires separable localization and activation functions of ATRIP.
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Nuñez, Estefanía, Irene Orera, Lorena Carmona-Rodríguez, José Ramón Paño, Jesús Vázquez i Fernando J. Corrales. "Mapping the Serum Proteome of COVID-19 Patients; Guidance for Severity Assessment". Biomedicines 10, nr 7 (13.07.2022): 1690. http://dx.doi.org/10.3390/biomedicines10071690.
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Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whose outbreak in 2019 led to an ongoing pandemic with devastating consequences for the global economy and human health. According to the World Health Organization, COVID-19 has affected more than 481 million people worldwide, with 6 million confirmed deaths. The joint efforts of the scientific community have undoubtedly increased the pace of production of COVID-19 vaccines, but there is still so much uncharted ground to cover regarding the mechanisms of SARS-CoV-2 infection, replication and host response. These issues can be approached by proteomics with unprecedented capacity paving the way for the development of more efficient strategies for patient care. In this study, we present a deep proteome analysis that has been performed on a cohort of 72 COVID-19 patients aiming to identify serum proteins assessing the dynamics of the disease at different age ranges. A panel of 53 proteins that participate in several functions such as acute-phase response and inflammation, blood coagulation, cell adhesion, complement cascade, endocytosis, immune response, oxidative stress and tissue injury, have been correlated with patient severity, suggesting a molecular basis for their clinical stratification. Eighteen protein candidates were further validated by targeted proteomics in an independent cohort of 84 patients including a group of individuals that had satisfactorily resolved SARS-CoV-2 infection. Remarkably, all protein alterations were normalized 100 days after leaving the hospital, which further supports the reliability of the selected proteins as hallmarks of COVID-19 progression and grading. The optimized protein panel may prove its value for optimal severity assessment as well as in the follow up of COVID-19 patients.
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Schuster, Peter. "From Self-Organization to Evolution of RNA Molecules: The Origin of Biological Information". Solid State Phenomena 97-98 (kwiecień 2004): 27–36. http://dx.doi.org/10.4028/www.scientific.net/ssp.97-98.27.
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Autocatalytic chemical reactions may lead to spatio-temporal patterns if processed under non-equilibrium conditions. The patterns disappear when the conditions change and information stored in these non-equilibrium structures is lost since precise reconstructions are impossible. Replication of molecules, in particular of polynucleotides RNA or DNA, is an autocatalytic process too. The storage of information in polynucleotide sequences, however, allows for reconstruction of the molecules under suitable conditions. Conservation of information in polymer sequences constitutes the basic difference between chemical and biological self-organization. Evolution of RNA molecules is considered as pattern formation in sequence space, which manifests itself as another pattern in the space of minimum-free-energy structures. In addition, optimization of RNA structures and properties is visualized as an evolutionary trial-and-error process. This process can be interpreted as a simple form of learning at the level of ensembles or populations of molecules. Evolutionary optimization of RNA molecules occurs in steps: Short adaptive periods are interrupted by long epochs of quasi-stationarity during which the mean replication rate of the populations is essentially constant. Understanding of evolution is largely facilitated through consideration of sequence-structure relation as a many-to-one or non-invertible mapping from sequence space into structure space. Neutrality of sequences with respect to structure formation is highly relevant for evolutionary optimization on rugged fitness landscapes.
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Yang, Jui-Pin, i Hui-Kai Su. "Integrated Resource Management for Fog Networks". Sensors 22, nr 6 (21.03.2022): 2404. http://dx.doi.org/10.3390/s22062404.
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In this paper, we consider integrated resource management for fog networks inclusive of intelligent energy perception, service level agreement (SLA) planning and replication-based hotspot offload (RHO). In the beginning, we propose an intelligent energy perception scheme which dynamically classifies the fog nodes into a hot set, a warm set or a cold set, based on their load conditions. The fog nodes in the hot set are responsible for a quality of service (QoS) guarantee and the fog nodes in the cold set are maintained at a low-energy state to save energy consumption. Moreover, the fog nodes in the warm set are used to balance the QoS guarantee and energy consumption. Secondly, we propose an SLA mapping scheme which effectively identifies the SLA elements with the same semantics. Finally, we propose a replication-based load-balancing scheme, namely RHO. The RHO can leverage the skewed access pattern caused by the hotspot services. In addition, it greatly reduces communication overheads because the load conditions are updated only when the load variations exceed a specific threshold. Finally, we use computer simulations to compare the performance of the RHO with other schemes under a variety of load conditions. In a word, we propose a comprehensive and feasible solution that contributes to the integrated resource management of fog networks.
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Tsanas, Athanasios, Max A. Little, Patrick E. McSharry i Lorraine O. Ramig. "Nonlinear speech analysis algorithms mapped to a standard metric achieve clinically useful quantification of average Parkinson's disease symptom severity". Journal of The Royal Society Interface 8, nr 59 (17.11.2010): 842–55. http://dx.doi.org/10.1098/rsif.2010.0456.
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The standard reference clinical score quantifying average Parkinson's disease (PD) symptom severity is the Unified Parkinson's Disease Rating Scale (UPDRS). At present, UPDRS is determined by the subjective clinical evaluation of the patient's ability to adequately cope with a range of tasks. In this study, we extend recent findings that UPDRS can be objectively assessed to clinically useful accuracy using simple, self-administered speech tests, without requiring the patient's physical presence in the clinic. We apply a wide range of known speech signal processing algorithms to a large database (approx. 6000 recordings from 42 PD patients, recruited to a six-month, multi-centre trial) and propose a number of novel, nonlinear signal processing algorithms which reveal pathological characteristics in PD more accurately than existing approaches. Robust feature selection algorithms select the optimal subset of these algorithms, which is fed into non-parametric regression and classification algorithms, mapping the signal processing algorithm outputs to UPDRS. We demonstrate rapid, accurate replication of the UPDRS assessment with clinically useful accuracy (about 2 UPDRS points difference from the clinicians' estimates, p < 0.001). This study supports the viability of frequent, remote, cost-effective, objective, accurate UPDRS telemonitoring based on self-administered speech tests. This technology could facilitate large-scale clinical trials into novel PD treatments.
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Mujiyo, M., Yosua Yoga Setyawan, Aktavia Herawati i Hery Widijanto. "The effect of land use on soil quality in Giriwoyo Sub-district, Wonogiri Regency". Journal of Degraded and Mining Lands Management 8, nr 2 (31.12.2020): 2559–68. http://dx.doi.org/10.15243/jdmlm.2021.082.2559.
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Determination of soil quality in Giriwoyo Sub-district, Wonogiri Regency, will generate a Soil Quality Index which can be used as a reference for soil cultivation for optimal productivity. This research was a descriptive exploratory with a survey approach. The survey area consisted of 12 land mapping units (LMU) with 3 replications for each LMU. Determination of LMU based on soil type, land use, slope and rainfall. The parameters used were BD (bulk density), porosity, organic C, pH, CEC (cation exchange capacity), BS (base saturation), available P, available K, total N, and MBC (microbial biomass carbon) that represented the physical, chemical and biological properties of the soil. Principal Component Analysis (PCA) analysis was performed to obtain the Minimum Data Set (MDS). The Soil Quality Index (SQI) at each LMU was calculated by multiplying the PCA result score (Wi) with the score for each selected indicator (Si). The result showed that the Soil Quality Index at each LMU was low. The highest Soil Quality Index was found in fields land use with an SQI of 0.34. The soil indicator that limited the soil quality was available P.
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Klostermann, André. "Does the Simon Effect Interfere with the Synergy Between Perception and Action?" Perceptual and Motor Skills 128, nr 4 (2.06.2021): 1765–84. http://dx.doi.org/10.1177/00315125211022917.
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Research suggests that – particularly – the execution of precision-demanding far-aiming tasks necessitates an optimal coupling between perception and action. In this regard, the duration of the last fixation before initiating movement – i.e., the Quiet Eye (QE) – has been functionally related to subsequent motor performance. In the current study, we investigated potential mechanisms of QE by applying the Simon paradigm – i.e., cognitive interferences evoked by stimulus-effect incompatibilities over response selection. To this end, we had participants throw balls as precisely as possible, either with their left or right hand (hands condition, HC) or at left or right targets (targets condition, TC), respectively. Via monaural auditory stimuli, participants received information about the hand side and the target side, respectively, either with compatible (i.e., congruent stimulus-effect side) or incompatible (i.e., incongruent stimulus-effect side) stimulus-effect mappings. Results showed that participants reacted slower and showed later first fixation onsets at the target in incompatible vs. compatible trials, thus, replicating and extending the classical Simon effect. Crucially, in the HC, there were earlier QE onsets and longer QE durations in incompatible (vs. compatible) trials, suggesting an inhibition of cognitive interferences over response selection to preserve motor performance. These findings are in line with attentional explanations of QE, suggesting optimized attentional control with efficient management of limited cognitive resources (optimal-attentional-control explanation) or with the inhibition of alternative response parametrization (inhibition explanation).
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Slapničar, Gašper, Jie Su i Wenjin Wang. "Fundamental and Practical Feasibility of Electrocardiogram Reconstruction from Photoplethysmogram". Sensors 24, nr 7 (25.03.2024): 2100. http://dx.doi.org/10.3390/s24072100.
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Electrocardiogram (ECG) reconstruction from contact photoplethysmogram (PPG) would be transformative for cardiac monitoring. We investigated the fundamental and practical feasibility of such reconstruction by first replicating pioneering work in the field, with the aim of assessing the methods and evaluation metrics used. We then expanded existing research by investigating different cycle segmentation methods and different evaluation scenarios to robustly verify both fundamental feasibility, as well as practical potential. We found that reconstruction using the discrete cosine transform (DCT) and a linear ridge regression model shows good results when PPG and ECG cycles are semantically aligned—the ECG R peak and PPG systolic peak are aligned—before training the model. Such reconstruction can be useful from a morphological perspective, but loses important physiological information (precise R peak location) due to cycle alignment. We also found better performance when personalization was used in training, while a general model in a leave-one-subject-out evaluation performed poorly, showing that a general mapping between PPG and ECG is difficult to derive. While such reconstruction is valuable, as the ECG contains more fine-grained information about the cardiac activity as well as offers a different modality (electrical signal) compared to the PPG (optical signal), our findings show that the usefulness of such reconstruction depends on the application, with a trade-off between morphological quality of QRS complexes and precise temporal placement of the R peak. Finally, we highlight future directions that may resolve existing problems and allow for reliable and robust cross-modal physiological monitoring using just PPG.
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Cavey, Andrew M. J., Jonathan M. Spector, Derek Ehrhardt, Theresa Kittle, Mills McNeill, P. Gregg Greenough i Thomas D. Kirsch. "Mississippi's Infectious Disease Hotline: A Surveillance and Education Model for Future Disasters". Prehospital and Disaster Medicine 24, nr 1 (luty 2009): 11–17. http://dx.doi.org/10.1017/s1049023x00006488.
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AbstractIntroduction:The potential for outbreaks of epidemic disease among displaced residents was a significant public health concern in the aftermath of Hurricane Katrina. In response, the Mississippi Department of Health (MDH) and the American Red Cross (ARC) implemented a novel infectious disease surveillance system, in the form of a telephone “hotline”, to detect and rapidly respond to health threats in shelters.Methods:All ARC-managed shelters in Mississippi were included in the surveillance system. A symptom-based, case reporting method was developed and distributed to shelter staff, who were linked with MDH and ARC professionals by a toll-free telephone service. Hotline staff investigated potential infectious disease outbreaks, provided assistance to shelter staff regarding optimal patient care, and helped facilitate the evaluation of ill evacuees by local medical personnel.Results:Forty-three shelters sheltering 3,520 evacuees participated in the program. Seventeen shelters made 29 calls notifying the hotline of the following cases: (1) fever (6 cases); (2) respiratory infections (37 cases); (3) bloody diarrhea (2 cases); (4) watery diarrhea (15 cases); and (5) other, including rashes (33 cases). Thirty-four of these patients were referred to a local physician or hospital for further diagnosis and disease management. Three cases of chickenpox were identified. No significant infectious disease outbreaks occurred and no deaths were reported.Conclusions:The surveillance system used direct verbal communication between shelter staff and hotline managers to enable more rapid reporting, mapping, investigation, and intervention, far beyond the capabilities of a more passive or paper-based system. It also allowed for immediate feedback and education for staff unfamiliar with the diseases and reporting process. Replication of this program should be considered during future disasters when health surveillance of a large, disseminated shelter population is necessary.
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Stefansson, Petter, Fredrik Karlsson, Magnus Persson i Carl Magnus Olsson. "Synthetic Generation of Passive Infrared Motion Sensor Data Using a Game Engine". Sensors 21, nr 23 (2.12.2021): 8078. http://dx.doi.org/10.3390/s21238078.
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Quantifying the number of occupants in an indoor space is useful for a wide variety of applications. Attempts have been made at solving the task using passive infrared (PIR) motion sensor data together with supervised learning methods. Collecting a large labeled dataset containing both PIR motion sensor data and ground truth people count is however time-consuming, often requiring one hour of observation for each hour of data gathered. In this paper, a method is proposed for generating such data synthetically. A simulator is developed in the Unity game engine capable of producing synthetic PIR motion sensor data by detecting simulated occupants. The accuracy of the simulator is tested by replicating a real-world meeting room inside the simulator and conducting an experiment where a set of choreographed movements are performed in the simulated environment as well as the real room. In 34 out of 50 tested situations, the output from the simulated PIR sensors is comparable to the output from the real-world PIR sensors. The developed simulator is also used to study how a PIR sensor’s output changes depending on where in a room a motion is carried out. Through this, the relationship between sensor output and spatial position of a motion is discovered to be highly non-linear, which highlights some of the difficulties associated with mapping PIR data to occupancy count.
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Schouten, Girmi, Wouter Jansen i Jan Steckel. "Simulation of Pulse-Echo Radar for Vehicle Control and SLAM". Sensors 21, nr 2 (13.01.2021): 523. http://dx.doi.org/10.3390/s21020523.
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Pulse-echo sensing is the driving principle behind biological echolocation as well as biologically-inspired sonar and radar sensors. In biological echolocation, a single emitter sends a self-generated pulse into the environment which reflects off objects. A fraction of these reflections are captured by two receivers as echoes, from which information about the objects, such as their position in 3D space, can be deduced by means of timing, intensity and spectral analysis. This is opposed to frequency-modulated continuous-wave radar, which analyses the shift in frequency of the returning signal to determine distance, and requires an array of antenna to obtain directional information. In this work, we present a novel simulator which can generate synthetic pulse-echo measurements for a simulated sensor in a virtual environment. The simulation is implemented by replicating the relevant physical processes underlying the pulse-echo sensing modality, while achieving high performance at update rates above 50 Hz. The system is built to perform design space exploration of sensor hardware and software, with the goals of rapid prototyping and preliminary safety testing in mind. We demonstrate the validity of the simulator by replicating real-world experiments from previous work. In the first case, a subsumption architecture vehicle controller is set to navigate an unknown environment using the virtual sensor. We see the same trajectory pattern emerge in the simulated environment rebuilt from the real experiment, as well as similar activation times for the high-priority behaviors (±1.9%), and low-priority behaviors (±0.2%). In a second experiment, the simulated signals are used as input to a biologically-inspired direct simultaneous mapping and localization (SLAM) algorithm. Using only path integration, 83% of the positional errors are larger than 10 m, while for the SLAM algorithm 95% of the errors are smaller than 3.2 m. Additionally, we perform design space exploration using the simulator. By creating a synthetic radiation pattern with increased spatiospectral variance, we are able to reduce the average localization error of the system by 11%. From these results, we conclude that the simulation is sufficiently accurate to be of use in developing vehicle controllers and SLAM algorithms for pulse-echo radar sensors.
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Badshah, Fazal, Kalim U. Tariq, Ahmed Henaish i Junaid Akhtar. "On some soliton structures for the perturbed nonlinear Schrödinger equation with Kerr law nonlinearity in mathematical physics". Mathematical Methods in the Applied Sciences, 19.12.2023. http://dx.doi.org/10.1002/mma.9837.
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The most important physical structure that is assumed to illustrate the geometry of optical soliton replication in optical fiber theory is the nonlinear Schrödinger equation (NLSE). Optical soliton generation in nonlinear optical fibers is a topic of great contemporary interest because of the numerous applications of ultrafast signal routing systems and short light pulses in communications. This analysis's main goal is to create a large number of soliton solutions for the dynamical model using a variety of contemporary analytical methods. This paper studies different soliton solutions to the perturbed NLSE with Kerr law nonlinearity using two sets of two distinct integration strategies: the mapping approach and the unified auxiliary equation method. The majority of solutions have been found as Jacobi elliptic functions with limiting ellipticity modulus values. Solitons like dark, bright, optical, lonely, and others are also retrieved. We were able to create various single‐type solutions with the help of these strategies. As a result, there is a variety of optical, bell‐shaped, single periodic, and multi‐periodic solutions. In order to validate the computations, the stability of the acquired findings must also be proven. The study provides a highly stunning and suitable strategy for combining numerous exciting wave demonstrations for more advanced models of the present era. Furthermore, we can assert that the outcomes reported here are unique and novel.
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Singh, Manrose, Kaitlin Raseley, Alexis M. Perez, Danny MacKenzie, Settapong T. Kosiyatrakul, Sanket Desai, Noelle Batista i in. "Elucidation of the molecular mechanism of the breakage-fusion-bridge (BFB) cycle using a CRISPR-dCas9 cellular model". Nucleic Acids Research, 28.08.2024. http://dx.doi.org/10.1093/nar/gkae747.
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Abstract Chromosome instability (CIN) is frequently observed in many tumors. The breakage-fusion-bridge (BFB) cycle has been proposed to be one of the main drivers of CIN during tumorigenesis and tumor evolution. However, the detailed mechanism for the individual steps of the BFB cycle warrants further investigation. Here, we demonstrate that a nuclease-dead Cas9 (dCas9) coupled with a telomere-specific single-guide RNA (sgTelo) can be used to model the BFB cycle. First, we show that targeting dCas9 to telomeres using sgTelo impedes DNA replication at telomeres and induces a pronounced increase of replication stress and DNA damage. Using Single-Molecule Telomere Assay via Optical Mapping (SMTA-OM), we investigate the genome-wide features of telomeres in the dCas9/sgTelo cells and observe a dramatic increase of chromosome end fusions, including fusion/ITS+ and fusion/ITS−. Consistently, we also observe an increase in the formation of dicentric chromosomes, anaphase bridges, and intercellular telomeric chromosome bridges (ITCBs). Utilizing the dCas9/sgTelo system, we uncover many interesting molecular and structural features of the ITCB and demonstrate that multiple DNA repair pathways are implicated in the formation of ITCBs. Our studies shed new light on the molecular mechanisms of the BFB cycle, which will advance our understanding of tumorigenesis, tumor evolution, and drug resistance.
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Xu, Yi, Meiling Xie i Shuhui Xiong. "Application of Virtual Reality Technology in Historical and Cultural Landscape Reproduction". Applied Mathematics and Nonlinear Sciences 9, nr 1 (1.01.2024). http://dx.doi.org/10.2478/amns-2024-1583.
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Abstract Virtual reality panoramic technology transcends the constraints of time and space, offering audiences immersive visual and auditory experiences that diminish the costs associated with exploring historical and cultural landscapes and enhance communication effectiveness. This study employs fisheye cameras to capture panoramic images of such landscapes. The collected images undergo correction via spherical projection and reflective planar unfolding mapping. Subsequently, an enhanced method for optimal stitching line selection is applied to ensure seamless transitions between spliced images. The process is completed by integrating image interpolation and projection algorithms to virtually recreate historical landscapes. Analytical assessment of the model’s reproduction effects focuses on point error and accuracy. A practical application involving a real historical and cultural landscape is examined, revealing a maximum control point deviation from the optical scan of 0.02m and a minimum of 0.0014m, which negligibly affects the landscape’s virtual representation. Reproducing an actual landscape image yielded a maximum measurement error of 0.02m, a minimum of 0.01m, and an average of 0.0175m, affirming the capability for precise replication. This paper introduces innovative approaches and methodologies for leveraging virtual reality technology in the accurate reproduction of historical and cultural landscapes, illustrating its practical utility and effectiveness.
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Bashit, Abdullah Al, Prakash Nepal, Theresa Connors, Derek H. Oakley, Bradley T. Hyman, Lin Yang i Lee Makowski. "Mapping the Spatial Distribution of Fibrillar Polymorphs in Human Brain Tissue". Frontiers in Neuroscience 16 (1.06.2022). http://dx.doi.org/10.3389/fnins.2022.909542.
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Alzheimer’s disease (AD) is a neurodegenerative disorder defined by the progressive formation and spread of fibrillar aggregates of Aβ peptide and tau protein. Polymorphic forms of these aggregates may contribute to disease in varying ways since different neuropathologies appear to be associated with different sets of fibrillar structures and follow distinct pathological trajectories that elicit characteristic clinical phenotypes. The molecular mechanisms underlying the spread of these aggregates in disease may include nucleation, replication, and migration all of which could vary with polymorphic form, stage of disease, and region of brain. Given the linkage between mechanisms of progression and distribution of polymorphs, mapping the distribution of fibrillar structures in situ has the potential to discriminate between mechanisms of progression. However, the means of carrying out this mapping are limited. Optical microscopy lacks the resolution to discriminate between polymorphs in situ, and higher resolution tools such as ssNMR and cryoEM require the isolation of fibrils from tissue, destroying relevant spatial information. Here, we demonstrate the use of scanning x-ray microdiffraction (XMD) to map the locations of fibrillar polymorphs of Aβ peptides and tau protein in histological thin sections of human brain tissue. Coordinated examination of serial sections by immunohistochemistry was used to aid in the interpretation of scattering patterns and to put the observations in a broader anatomical context. Scattering from lesions in tissue shown to be rich in Aβ fibrils by immunohistochemistry exhibited scattering patterns with a prototypical 4.7 Å cross-β peak, and overall intensity distribution that compared well with that predicted from high resolution structures. Scattering from lesions in tissue with extensive tau pathology also exhibited a 4.7 Å cross-β peak but with intensity distributions that were distinct from those seen in Aβ-rich regions. In summary, these observations demonstrate that XMD is a rich source of information on the distribution of fibrillar polymorphs in diseased human brain tissue. When used in coordination with neuropathological examination it has the potential to provide novel insights into the molecular mechanisms underlying disease.
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Liu, Liang, Wangqi Mao, Xinyu Gao, Chenglin He, Zilan Tang, Hao Chang, Long Zhang, Xiaoxia Wang, Hongxing Dong i Anlian Pan. "Vertically Aligned Perovskite Laser Arrays for High‐Capacity Anticounterfeiting Labels". Laser & Photonics Reviews, 15.12.2023. http://dx.doi.org/10.1002/lpor.202301006.
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AbstractPhysically unclonable functions (PUFs) have emerged as the most effective method against counterfeiting, leveraging the intrinsic randomness of objects to avoid data replication. However, despite their efficacy, the complexity and high cost of most PUF‐based counterfeiting labels hinder their practical application. Here, a high‐capacity PUF label based on vertically aligned perovskite nanowire (NW) arrays is demonstrated. The NW arrays are conveniently constructed using a low‐cost solution process using an anodized aluminum oxide template. Each pixel within the label is composed of closely packed CsPbBr3 NW arrays of different lengths, resulting in varied lasing signals. The collected signal of each pixel emerged from the lasing output of the NW arrays, generating high‐density and nonuniform multiple‐mode lasing to facilitate information encoding. A quaternary encoding mechanism is used to encode the number of laser modes per pixel. Impressively, it exhibits a mapping resolution of 1600 pixels within 400 µm2, achieving an impressive encoding capacity (1.97 × 10963) and a pixel density (4 bits µm−2) in this compact area. This work shows a promising approach for anticounterfeiting applications because of its simplicity, low cost, and high encoding capacity.
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Vincent, Kathleen L., Patrice A. Frost, Massoud Motamedi, Edward J. Dick, Jingna Wei, Jinping Yang, Robert White i Marie-Claire Gauduin. "High-Resolution Quantitative Mapping of Macaque Cervicovaginal Epithelial Thickness: Implications for Mucosal Vaccine Delivery". Frontiers in Immunology 12 (28.06.2021). http://dx.doi.org/10.3389/fimmu.2021.660524.
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Vaginal mucosal surfaces naturally offer some protection against sexually transmitted infections (STIs) including Human Immunodeficiency Virus-1, however topical preventative medications or vaccine designed to boost local immune responses can further enhance this protection. We previously developed a novel mucosal vaccine strategy using viral vectors integrated into mouse dermal epithelium to induce virus-specific humoral and cellular immune responses at the site of exposure. Since vaccine integration occurs at the site of cell replication (basal layer 100-400 micrometers below the surface), temporal epithelial thinning during vaccine application, confirmed with high resolution imaging, is desirable. In this study, strategies for vaginal mucosal thinning were evaluated noninvasively using optical coherence tomography (OCT) to map reproductive tract epithelial thickness (ET) in macaques to optimize basal layer access in preparation for future effective intravaginal mucosal vaccination studies. Twelve adolescent female rhesus macaques (5-7kg) were randomly assigned to interventions to induce vaginal mucosal thinning, including cytobrush mechanical abrasion, the chemical surfactant spermicide nonoxynol-9 (N9), the hormonal contraceptive depomedroxyprogesterone acetate (DMPA), or no intervention. Macaques were evaluated at baseline and after interventions using colposcopy, vaginal biopsies, and OCT imaging, which allowed for real-time in vivo visualization and measurement of ET of the mid-vagina, fornices, and cervix. P value ≤0.05 was considered significant. Colposcopy findings included pink, rugated tissue with variable degrees of white-tipped, thickened epithelium. Baseline ET of the fornices was thinner than the cervix and vagina (p<0.05), and mensing macaques had thinner ET at all sites (p<0.001). ET was decreased 1 month after DMPA (p<0.05) in all sites, immediately after mechanical abrasion (p<0.05) in the fornix and cervix, and after two doses of 4% N9 (1.25ml) applied over 14 hrs in the fornix only (p<0.001). Histological assessment of biopsied samples confirmed OCT findings. In summary, OCT imaging allowed for real time assessment of macaque vaginal ET. While varying degrees of thinning were observed after the interventions, limitations with each were noted. ET decreased naturally during menses, which may provide an ideal opportunity for accessing the targeted vaginal mucosal basal layers to achieve the optimum epithelial thickness for intravaginal mucosal vaccination.
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Garrott, Kara E., Anastasia Wengrowski, Hanyu Zhang, Jack Rogers i Matthew Kay. "Abstract 401: Shortening of Action Potential Duration With Increased Work in Contracting Rabbit Heart". Circulation Research 117, suppl_1 (17.07.2015). http://dx.doi.org/10.1161/res.117.suppl_1.401.
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Studying heart function in contracting hearts at higher workloads provides crucial knowledge of cardiac performance in high-stress situations. Ratiometric optical mapping of fully loaded hearts is a novel method to study electrical activity while replicating in vivo energy consumption. We predict that an imbalance between energy supply and demand during increased work and hypoxia will manifest in shortened action potential duration (APD), especially in the more physiologically-relevant bi-ventricular (BiV) working heart. Rabbit hearts were perfused with oxygenated Krebs-Henseleit solution in unloaded Langendorff and fully-loaded BiV mode. Epicardial action potentials (APs) were measured using optical mapping of Di-4-ANEPPS. Excitation ratiometry using 450 and 505 nm illumination on alternate camera frames together with motion tracking removed motion artifact. Aortic pressure, left atrial preload, and LVDP was measured. A range of workloads were studied by pacing at 330, 220, and 170 ms cycle length (CL). Gradual hypoxia was induced by bubbling with N2 gas. In Langendorff mode, the APD was 137.67±4.29 ms, 113.44±7.89 ms, and 106.44±0.44 ms at CL of 330ms, 220ms, and 170ms, respectively, while in BiV mode, the APD was 106.56±13.03 ms, 78.00±2.33 ms, and 69.33±0.77 ms. Aortic pressure dropped from NSR in BiV hearts by 1.26% at 330ms, 4.11% at 220ms, and 11.65% at 170ms CL. Shortening of APD, independent of restitution, with increasing HR indicates an imbalance of energy supply and demand with greater workload. KATP channels are implicated. This novel method of optical mapping reveals important implications of electrophysiological changes during high-stress situations.
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Schirmeisen, Kamila, Karel Naiman, Karine Fréon, Laetitia Besse, Shrena Chakraborty, Anissia Ait Saada, Antony M. Carr, Karol Kramarz i Sarah A. E. Lambert. "SUMO protease and proteasome recruitment at the nuclear periphery differently affect replication dynamics at arrested forks". Nucleic Acids Research, 25.06.2024. http://dx.doi.org/10.1093/nar/gkae526.
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Abstract Nuclear pore complexes (NPCs) have emerged as genome organizers, defining a particular nuclear compartment enriched for SUMO protease and proteasome activities, and act as docking sites for the repair of DNA damage. In fission yeast, the anchorage of perturbed replication forks to NPCs is an integral part of the recombination-dependent replication restart mechanism (RDR) that resumes DNA synthesis at terminally dysfunctional forks. By mapping DNA polymerase usage, we report that SUMO protease Ulp1-associated NPCs ensure efficient initiation of restarted DNA synthesis, whereas proteasome-associated NPCs sustain the progression of restarted DNA polymerase. In contrast to Ulp1-dependent events, this last function is not alleviated by preventing SUMO chain formation. By analyzing the role of the nuclear basket, the nucleoplasmic extension of the NPC, we reveal that the activities of Ulp1 and the proteasome cannot compensate for each other and affect the dynamics of RDR in distinct ways. Our work probes two distinct mechanisms by which the NPC environment ensures optimal RDR, both controlled by different NPC components.
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Kaur, Satwinder, i Mehak Aggarwal. "Extended Balanced Scheduler with Clustering and Rep- lication for Data Intensive Scientific Workflow Applications in Cloud Computing". Journal of Electronic Research and Application 2, nr 3 (13.06.2018). http://dx.doi.org/10.26689/jera.v2i3.380.
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Cloud computing is an advance computing model using which several applications, data and countless IT services are provided over the Internet. Task scheduling plays a crucial role in cloud computing systems. The issue of task scheduling can be viewed as the finding or searching an optimal mapping/assignment of set of subtasks of different tasks over the available set of resources so that we can achieve the desired goals for tasks. With the enlargement of users of cloud the tasks need to be scheduled. Cloud’s performance depends on the task scheduling algorithms used. Numerous algorithms have been submitted in the past to solve the task scheduling problem for heterogeneous network of computers. The existing research work proposes different methods for data intensive applications which are energy and deadline aware task scheduling method. As scientific workflow is combination of fine grain and coarse grain task. Every task scheduled to VM has system overhead. If multiple fine grain task are executing in scientific workflow, it increase the scheduling overhead. To overcome the scheduling overhead, multiple small tasks has been combined to large task, which decrease the scheduling overhead and improve the execution time of the workflow. Horizontal clustering has been used to cluster the fine grained task further replication technique has been combined. The proposed scheduling algorithm improves the performance metrics such as execution time and cost. Further this research can be extended with improved clustering technique and replication methods.
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Rubiola, Andrea, Steven Cunnington i Stefano Camera. "Baryon acoustic oscillations from H i intensity mapping: The importance of cross-correlations in the monopole and quadrupole". Monthly Notices of the Royal Astronomical Society, 6.09.2022. http://dx.doi.org/10.1093/mnras/stac2484.
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Abstract Cosmological parameter estimation in the post-reionisation era via neutral hydrogen radio emission (H i), is among the key science goals of the forthcoming SKA Observatory (SKAO). This paper explores detection capability for baryon acoustic oscillations (BAO) with a suite of 100 simulations introducing the main limitations from foreground contamination and poor angular resolution caused by the radio telescope beam. Such broad single-dish beam representing a serious challenge for BAO detection with H i intensity mapping, we investigate a multipole expansion approach as a means for mitigating such limitations. We also showcase the gains made from cross-correlating the H i intensity mapping data with an overlapping spectroscopic galaxy survey, aiming to test potential synergies between the SKA Project and other future cosmological experiments at optical/near-infrared wavelengths. For our ∼ 4 000 deg2 data set at z = 0.9, replicating the essential features of an SKAO H i intensity mapping survey, we were able to achieve a ∼ 4.5σ detection of BAO features in auto-correlation despite the dominant beam effect. Cross-correlation with an overlapping galaxy survey can increase this to a ∼ 6σ detection. Furthermore, including the power spectrum quadrupole besides the monopole in a joint fit can approximately double the BAO detection significance. Despite not implementing a radial-only P(k∥) analysis in favour of the three-dimensional P(k) and its multipoles, we were still able to obtain robust constraints on the radial Alcock-Paczynski parameter, whereas the perpendicular parameter remains unconstrained and prior dominated due to beam effects.
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van Agteren, Joep, Matthew Iasiello, Kathina Ali, Daniel B. Fassnacht, Gareth Furber, Lydia Woodyatt, Alexis Howard i Michael Kyrios. "Using the Intervention Mapping Approach to Develop a Mental Health Intervention: A Case Study on Improving the Reporting Standards for Developing Psychological Interventions". Frontiers in Psychology 12 (5.10.2021). http://dx.doi.org/10.3389/fpsyg.2021.648678.
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Replicating or distilling information from psychological interventions reported in the scientific literature is hindered by inadequate reporting, despite the existence of various methodologies to guide study reporting and intervention development. This article provides an in-depth explanation of the scientific development process for a mental health intervention, and by doing so illustrates how intervention development methodologies can be used to improve development reporting standards of interventions. Intervention development was guided by the Intervention Mapping approach and the Theoretical Domains Framework. It relied on an extensive literature review, input from a multi-disciplinary group of stakeholders and the learnings from projects on similar psychological interventions. The developed programme, called the “Be Well Plan”, focuses on self-exploration to determine key motivators, resources and challenges to improve mental health outcomes. The programme contains an online assessment to build awareness about one’s mental health status. In combination with the exploration of different evidence-based mental health activities from various therapeutic backgrounds, the programme teaches individuals to create a personalised mental health and wellbeing plan. The use of best-practice intervention development frameworks and evidence-based behavioural change techniques aims to ensure optimal intervention impact, while reporting on the development process provides researchers and other stakeholders with an ability to scientifically interrogate and replicate similar psychological interventions.
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Jassim, Hussam Hameed, Hassan Ali Nedaie, Nooshin Banaee, Ghazale Geraily, Ali Kazemian i Danial Seifi Makrani. "Evaluation of the geometric and dosimetric accuracies of deformable image registration of targets and critical organs in prostate CBCT‐guided adaptive radiotherapy". Journal of Applied Clinical Medical Physics, 13.09.2024. http://dx.doi.org/10.1002/acm2.14490.
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AbstractPurposeKilovoltage cone beam computed tomography (kVCBCT)‐guided adaptive radiation therapy (ART) uses daily deformed CT (dCT), which is generated automatically through deformable registration methods. These registration methods may perform poorly in reproducing volumes of the target organ, rectum, and bladder during treatment. We analyzed the registration errors between the daily kVCBCTs and corresponding dCTs for these organs using the default optical flow algorithm and two registration procedures. We validated the effectiveness of these registration methods in replicating the geometry for dose calculation on kVCBCT for ART.MethodsWe evaluated three deformable image registration (DIR) methods to assess their registration accuracy and dose calculation effeciency in mapping target and critical organs. The DIR methods include (1) default intensity‐based deformable registration, (2) hybrid deformable registration, and (3) a two‐step deformable registration process. Each technique was applied to a computerized imaging reference system (CIRS) phantom (Model 062 M) and to five patients who received volumetric modulated arc therapy to the prostate. Registration accuracy was assessed using the 95% Hausdorff distance (HD95) and Dice similarity coefficient (DSC), and each method was compared with the intensity‐based registration method. The improvement in the dCT image quality of the CIRS phantom and five patients was assessed by comparing dCT with kVCBCT. Image quality quantitative metrics for the phantom included the signal‐to‐noise ratio (SNR), uniformity, and contrast‐to‐noise ratio (CNR), whereas those for the patients included the mean absolute error (MAE), mean error, peak signal‐to‐noise ratio (PSNR), and structural similarity index measure (SSIM). To determine dose metric differences, we used a dose‐volume histogram (DVH) and 3.0%/0.3 mm gamma analysis to compare planning computed tomography (pCT) and kVCBCT recalculations with restimulated CT images used as a reference.ResultsThe dCT images generated by the hybrid (dCTH) and two‐step (dCTC) registration methods resulted in significant improvements compared to kVCBCT in the phantom model. Specifically, the SNR improved by 107% and 107.2%, the uniformity improved by 90% and 75%, and the CNR improved by 212.2% and 225.6 for dCTH and dCTC methods, respectively. For the patient images, the MAEs improved by 98% and 94%, the PSNRs improved by 16.3% and 22.9%, and the SSIMs improved by 1% and 1% in the dCTH and dCTC methods, respectively. For the geometric evaluation, only the two‐step registration method improved registration accuracy. The dCTH method yielded an average HD95 of 12 mm and average DSC of 0.73, whereas dCTC yielded an average HD95 of 2.9 mm and average DSC of 0.902. The DVH showed that the dCTC‐based dose calculations differed by <2% from the expected results for treatment targets and volumes of organs at risk. Additionally, gamma indices for dCTC‐based treatment plans were >95% at all points, whereas they were <95% for kVCBCT‐based treatment plans.ConclusionThe two‐step registration method outperforms the intensity‐based and hybrid registration methods. While the hybrid and two‐step‐based methods improved the image quality of kVCBCT in a linear accelerator, only the two‐step method improved the registration accuracy of the corresponding structures among the pCT and kVCBCT datasets. A two‐step registration process is recommended for applying kVCBCT to ART, which achieves better registration accuracy for local and global image structures. This method appears to be beneficial for radiotherapy dose calculation in patients with pelvic cancer.