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Scientific Reports Feb 2024In this paper, an automatic design method is proposed for unit cell in spoof surface plasmon polaritons (SSPP) with an almost arbitrary dispersion curve. In this method,...
In this paper, an automatic design method is proposed for unit cell in spoof surface plasmon polaritons (SSPP) with an almost arbitrary dispersion curve. In this method, the pixel configuration is considered for the unit cell and, by using the binary particle swarm optimization method, the proper topology of the unit cell is explored so as to reach the target dispersion curve. Unlike the traditional method of controlling the dispersion curve, which is performed based on changing the geometric parameters of the predetermined unit cell, in this method, there is no need to know the shape of the unit cell, and the dispersion curve of the modes of SSPP unit cell can be controlled independently with more freedom. Two unit cell samples are designed in order to show the efficiency of the procedure. In the first sample, the dispersion curve is designed to have the lowest asymptotic frequency; in the second sample, the dispersion curve of the second mode is controlled independently from the first mode and is changed arbitrarily. SSPP transmission lines which are related to the unit cells of the two samples are designed, and it is demonstrated that measurement and simulation results are greatly in line with each other.
PubMed: 38369559
DOI: 10.1038/s41598-024-52842-6 -
PeerJ 2024Metabarcoding is a powerful tool, increasingly used in many disciplines of environmental sciences. However, to assign a taxon to a DNA sequence, bioinformaticians need...
Metabarcoding is a powerful tool, increasingly used in many disciplines of environmental sciences. However, to assign a taxon to a DNA sequence, bioinformaticians need to choose between different strategies or parameter values and these choices sometimes seem rather arbitrary. In this work, we present a case study on ITS2 and databases used to identify pollen collected by bees in Belgium. We blasted a random sample of sequences from the reference database against the remainder of the database using different strategies and compared the known taxonomy with the predicted one. This cross-validation (CV) approach proved to be an easy yet powerful way to (1) assess the relative accuracy of taxonomic predictions, (2) define rules to discard dubious taxonomic assignments and (3) provide a more objective basis to choose the best strategy. We obtained the best results with the best blast hit (best bit score) rather than by selecting the majority taxon from the top 10 hits. The predictions were further improved by favouring the most frequent taxon among those with tied best bit scores. We obtained better results with databases containing the full sequences available on NCBI rather than restricting the sequences to the region amplified by the primers chosen in our study. Leaked CV showed that when the true sequence is present in the database, blast might still struggle to match the right taxon at the species level, particularly with . Classical 10-fold CV-where the true sequence is removed from the database-offers a different yet more realistic view of the true error rates. Taxonomic predictions with this approach worked well up to the genus level, particularly for ITS2 (5-7% of errors). Using a database containing only the local flora of Belgium did not improve the predictions up to the genus level for local species and made them worse for foreign species. At the species level, using a database containing exclusively local species improved the predictions for local species by ∼12% but the error rate remained rather high: 25% for ITS2 and 42% for . Foreign species performed worse even when using a world database (59-79% of errors). We used classification trees and GLMs to model the % of errors . identity and consensus scores and determine appropriate thresholds below which the taxonomic assignment should be discarded. This resulted in a significant reduction in prediction errors, but at the cost of a much higher proportion of unassigned sequences. Despite this stringent filtering, at least 1/5 sequences deemed suitable for species-level identification ultimately proved to be misidentified. An examination of the variability in prediction accuracy between plant families showed that outperformed ITS2 for only two of the 27 families examined, and that the % correct species-level assignments were much better for some families (. 95% for Sapindaceae) than for others (. 35% for Salicaceae).
Topics: Bees; Animals; DNA Barcoding, Taxonomic; Pollen; Plants; Databases, Factual; Belgium
PubMed: 38313030
DOI: 10.7717/peerj.16567 -
International Journal of Infectious... Mar 2024Identifying patients with COVID-19 who are at risk of poor evolution is key to early decide on their hospitalization. We evaluated the combined impact of nucleocapsid...
OBJECTIVES
Identifying patients with COVID-19 who are at risk of poor evolution is key to early decide on their hospitalization. We evaluated the combined impact of nucleocapsid (N)-antigenemia profiled by a rapid test and antibodies against the S1 subunit of the SARS-CoV S protein (S1) on the hospitalization risk of patients with COVID-19.
METHODS
N-antigenemia and anti-S1 antibodies were profiled at admission to the emergency department in 146 patients with COVID-19 using the Panbio® antigen Rapid Test and the SARS-CoV-2 immunoglobulin G II Quant/SARS-CoV-2 immunoglobulin G assay from Abbott. A multivariable analysis was used to evaluate the impact of these factors on hospitalization.
RESULTS
Patients with a positive N-antigen test in plasma and anti-S1 levels <2821 arbitrary units/mL needed hospitalization more frequently (20 of 23, 87%). A total of 20 of 71 (28.2%) of those showing a negative N-antigen test and anti-S1 ≥2821 arbitrary units/mL were hospitalized for 18 of 52 (34.6%) of the patients with only one of these conditions. Patients with a positive N-antigen test and low antibody levels showed an odds ratio, 95% confidence interval, and P-value for hospitalization of 18.21, 2.74-121.18, and 0.003, respectively, and exhibited the highest mortality (30.4%).
CONCLUSIONS
Simultaneous profiling of a rapid N-antigen test in plasma and anti-S1 levels could help to early identify patients with COVID-19 needing hospitalization.
Topics: Humans; COVID-19; SARS-CoV-2; Antibodies, Viral; Immunoglobulin G; Hospitalization
PubMed: 38311026
DOI: 10.1016/j.ijid.2024.01.018 -
Metabolites Jan 2024Peyronie's disease (PD) is a chronic inflammatory disease affecting the penile albuginea. Oxidative stress (OS) is important for the development of the disease;...
Peyronie's disease (PD) is a chronic inflammatory disease affecting the penile albuginea. Oxidative stress (OS) is important for the development of the disease; therefore, it seemed interesting to us to directly measure OS at both the site of the disease and in peripheral blood. For a precise OS study, it is necessary to evaluate not only the single results of the total oxidant status (TOS) and total antioxidant status (TAS) but also their ratio: OS index (OSI) (arbitrary unit) = TOS/TAS × 100. This study included 49 PD patients examined and diagnosed in our Peyronie's care center and a control group of 50 cases. We collected blood samples from both the penis and a vein in the upper extremity; we used d-ROMs and PAT-test (FRAS kit) for OS measurement. Pearson's study found a statistical correlation between penile OSI values and PD plaque volumes: -value = 0.002. No correlation was found between systemic OSI values and PD plaque volumes: -value = 0.27. Penile OSI values were significantly reduced after the elimination of the PD plaque ( < 0.00001). The mean value of the penile OSI indices in the PD patients after plaque elimination corresponded to 0.090 ± 0.016 ( = 0.004). The comparison between the penile OSI values of the PD patients (with plaque elimination) and the control group revealed no statistically significant differences ( = 0.130). The absence of a correlation between Peyronie's plaque volume and systemic OSI values indicates that it is preferable to carry out the OS study by taking a sample directly from the site of the disease. By carrying out a penile OSI study, it would be possible to obtain a precise plaque-volume-dependent oxidative marker. Even if the study did not demonstrate any correlation between OSI indices and anxious-depressive state, we detected a high prevalence of anxiety (81.6%) and depression (59.1%) in PD patients.
PubMed: 38248858
DOI: 10.3390/metabo14010055 -
Discrete & Computational Geometry 2024Let be a set of in the plane, so that every site has an . Let be the defined by , i.e., the graph with vertex set and an edge between two distinct sites if and...
Let be a set of in the plane, so that every site has an . Let be the defined by , i.e., the graph with vertex set and an edge between two distinct sites if and only if the disks with centers , and radii , intersect. Our goal is to design data structures that maintain the connectivity structure of as sites are inserted and/or deleted in . First, we consider , i.e., we fix , for all sites . For this case, we describe a data structure that has amortized update time and query time. Second, we look at disk graphs , i.e., for all , we have , for a parameter that is known in advance. Here, we not only investigate the fully dynamic case, but also the incremental and the decremental scenario, where only insertions or only deletions of sites are allowed. In the fully dynamic case, we achieve amortized expected update time and query time . This improves the currently best update time by a factor of . In the incremental case, we achieve logarithmic dependency on , with a data structure that has amortized query time and amortized expected update time, where denotes the inverse Ackermann function. For the decremental setting, we first develop an efficient decremental data structure: given two sets and of disks in the plane, we can delete disks from , and upon each deletion, we receive a list of all disks in that no longer intersect the union of . Using this data structure, we get decremental data structures with a query time of that supports deletions in overall expected time for disk graphs with bounded radius ratio and overall expected time for disk graphs with arbitrary radii, assuming that the deletion sequence is oblivious of the internal random choices of the data structures.
PubMed: 38192901
DOI: 10.1007/s00454-023-00621-x -
Science & Justice : Journal of the... Jan 2024In recent years, numerous studies have examined the chemical compounds of petrol and petrol data for forensic research. Standard quantitative methods often assume that...
In recent years, numerous studies have examined the chemical compounds of petrol and petrol data for forensic research. Standard quantitative methods often assume that the variables or compounds do not have compositional constraints or are not part of a constrained whole, operating within an Euclidean vector space. However, chemical compounds are typically part of a whole, and the appropriate vector space for their analysis is the simplex. Biased and arbitrary results result when statistical analysis are applied on such data without proper pre-processing of such data. Compositional analysis of data has not yet been considered in forensic science. Therefore, we compare classical statistical analysis as applied in forensic research and the new proposed paradigm of compositional data analysis (CoDa). It is demonstrated how such analysis improves the analysis in petrol and forensic science. Our study shows how principal component analysis (PCA) and classification results are affected by the preprocessing steps performed on the raw data. Our results indicate that results from a log ratio analysis provides a better separation between subgroups of the data and leads to an easier interpretation of the results. In addition, with a compositional analysis a higher classification accuracy is obtained. Even a non-linear classification method - in our case a random forest - was shown to perform poorly when applied without using compositional methods. Moreover, normalization of samples due to laboratory/unit-of-measurement effects is no longer necessary, since the composition of an observation is in compositional thinking equivalent to a multiple of it, because the used (log) ratios on raw and log ratio transformed data are equal. Petrol data from different petrol stations in Brazil are used for the demonstration. This data is highly susceptible to counterfeit petrol. Forensic analysis of its chemical elements requires non-biased statistical analysis designed for compositional data to detect fraud. Based on these results, we recommend the use of compositional data methods for gasoline and petrol chemical element analysis and gasoline product characterization, authentication and fraud detection in forensic sciences.
PubMed: 38182317
DOI: 10.1016/j.scijus.2023.11.003 -
Materials (Basel, Switzerland) Dec 2023In this paper, the scope of discrete asymptotic homogenization employing voxel (cartesian) mesh discretization is expanded to estimate high fidelity effective properties...
In this paper, the scope of discrete asymptotic homogenization employing voxel (cartesian) mesh discretization is expanded to estimate high fidelity effective properties of any periodic heterogeneous media with arbitrary Bravais's lattice symmetry, including those with non-orthogonal periodic bases. A framework was developed in Python with a proposed fast-nearest neighbour algorithm to accurately estimate the periodic boundary conditions of the discretized representative volume element of the lattice unit cell. Convergence studies are performed, and numerical errors caused by both voxel meshing and periodic boundary condition approximation processes are discussed in detail. It is found that the numerical error in periodicity approximation is cyclically dependent on the number of divisions performed during the meshing process and, thus, is minimized with a refined voxel mesh. Validation studies are performed by comparing the elastic properties of 2D hexagon lattices with orthogonal and non-orthogonal bases. The developed methodology was also applied to derive the effective properties of several lattice topologies, and variation of their anisotropic macroscopic properties with relative densities is presented as material selection charts.
PubMed: 38138704
DOI: 10.3390/ma16247562 -
Sensors (Basel, Switzerland) Nov 2023Most of the existing metasurfaces are effective for the incident wave with the specific circularly polarized (CP) or linearly polarized (LP) state, that is the...
Most of the existing metasurfaces are effective for the incident wave with the specific circularly polarized (CP) or linearly polarized (LP) state, that is the polarization-sensitive metasurface. This drawback dramatically hinders the practical use of the metasurface. Herein, this paper presents a strategy of polarization-insensitive transmissive microwave metasurfaces to manipulate the incident wave with arbitrary CP and LP states. The metasurface consists of polarization-insensitive unit cells. For the left circularly polarized (LCP) and right circularly polarized (RCP) incident waves, the same abrupt phase covering 0° to 360° can be realized by combining the Pancharatnam-Berry (PB) and resonant phases. As the arbitrary LP wave can decompose into the LCP and RCP waves, metasurfaces consisting of designed unit cells are valid for any polarization states. The polarization-insensitive transmissive microwave metalens and orbital angular momentum multiplexing metasurface working at 23 GHz are devised for verification. Simulation and measurement results verify the availability of the approach. The proposed method is suitable for designing microwave-transmissive metasurfaces capable of polarization insensitivity.
PubMed: 38067786
DOI: 10.3390/s23239413 -
Proceedings of the National Academy of... Dec 2023Tools are objects that are manipulated by agents with the intention to cause an effect in the world. We show that the cognitive capacity to understand tools is present...
Tools are objects that are manipulated by agents with the intention to cause an effect in the world. We show that the cognitive capacity to understand tools is present in young infants, even if these tools produce arbitrary, causally opaque effects. In experiments 1-2, we used pupillometry to show that 8-mo-old infants infer an invisible causal contact to account for the-otherwise unexplained-motion of a ball. In experiments 3, we probed 8-mo-old infants' account of a state change event (flickering of a cube) that lies outside of the explanatory power of intuitive physics. Infants repeatedly watched an intentional agent launch a ball behind an occluder. After a short delay, a cube, positioned at the other end of the occluder began flickering. Rare unoccluded events served to probe infants' representation of what happened behind the occluder. Infants exhibited larger pupil dilation, signaling more surprise, when the ball stopped before touching the cube, than when it contacted the cube, suggesting that infants inferred that the cause of the state change was contact between the ball and the cube. This effect was canceled in experiment 4, when an inanimate sphere replaced the intentional agent. Altogether, results suggest that, in the infants' eyes, a ball (an inanimate object) has the power to cause an arbitrary state change, but only if it inherits this power from an intentional agent. Eight-month-olds are thus capable of representing complex event structures, involving an intentional agent causing a change with a tool.
Topics: Infant; Humans; Intention; Intuition; Eye
PubMed: 38064512
DOI: 10.1073/pnas.2309669120 -
Gynecologic Oncology Jan 2024We evaluated usability of single base substitution signature 3 (Sig3) as a biomarker for homologous recombination deficiency (HRD) in tubo-ovarian high-grade serous... (Clinical Trial)
Clinical Trial Observational Study
OBJECTIVES
We evaluated usability of single base substitution signature 3 (Sig3) as a biomarker for homologous recombination deficiency (HRD) in tubo-ovarian high-grade serous carcinoma (HGSC).
MATERIALS AND METHODS
This prospective observational trial includes 165 patients with advanced HGSC. Fresh tissue samples (n = 456) from multiple intra-abdominal areas at diagnosis and after neoadjuvant chemotherapy (NACT) were collected for whole-genome sequencing. Sig3 was assessed by fitting samples independently with COSMIC v3.2 reference signatures. An HR scar assay was applied for comparison. Progression-free survival (PFS) and overall survival (OS) were studied using Kaplan-Meier and Cox regression analysis.
RESULTS
Sig3 has a bimodal distribution, eliminating the need for an arbitrary cutoff typical in HR scar tests. Sig3 could be assessed from samples with low (10%) cancer cell proportion and was consistent between multiple samples and stable during NACT. At diagnosis, 74 (45%) patients were HRD (Sig3+), while 91 (55%) were HR proficient (HRP, Sig3-). Sig3+ patients had longer PFS and OS than Sig3- patients (22 vs. 13 months and 51 vs. 34 months respectively, both p < 0.001). Sig3 successfully distinguished the poor prognostic HRP group among BRCAwt patients (PFS 19 months for Sig3+ and 13 months for Sig3- patients, p < 0.001). However, Sig3 at diagnosis did not predict chemoresponse anymore in the first relapse. The patient-level concordance between Sig3 and HR scar assay was 87%, and patients with HRD according to both tests had the longest median PFS.
CONCLUSIONS
Sig3 is a prognostic marker in advanced HGSC and useful tool in patient stratification for HRD.
Topics: Female; Humans; Cicatrix; Cystadenocarcinoma, Serous; Ovarian Neoplasms; Prognosis; Progression-Free Survival
PubMed: 38061276
DOI: 10.1016/j.ygyno.2023.11.027