Global Characterization Research Articles

Acoustics in Baroque Catholic Church Spaces

After the Council of Trent (1545–1563), the Catholic Church undertook a profound renovation, which affected the spatial configuration of the churches to adjust to the spirit of the Counter-Reformation. The acoustic cultural heritage in these spaces have been studied by different researchers, proposing the joint analysis of 66 Catholic churches from the Baroque period. This study delves into the global characterisation of the sample and establishes correlations between geometric and acoustic parameters. From the acoustic analysis, it is clear that the central floor typology, as opposed to Latin cross churches, presents better average values of musical clarity in relation to their volume. The analysis of the relationship between acoustic and geometric parameters, when the sample of churches is discriminated by typology, allows for the establishment of appropriate correlations for Latin cross floor plans, single naves and basilicas, but not when the analysis is carried out for the entire sample. These correlations are a tool that allows us to evaluate acoustic parameters not measured in situ in Catholic churches of the Baroque period in a predictive way as a function of other measured acoustic or geometric parameters.

Periodic derived Hall algebras of hereditary abelian categories

Let m be a positive integer and Dm(A) be the m-periodic derived category of a finitary hereditary abelian category A. Applying the derived Hall numbers of the bounded derived category Db(A), we define an m-periodic extended derived Hall algebra for Dm(A), and use it to give a global, unified and explicit characterization for the algebra structure of Bridgeland's Hall algebra of periodic complexes. Moreover, we also provide an explicit characterization for the odd periodic derived Hall algebra of A defined by Xu-Chen [24].

Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries.

Somatic mutations arise and accumulate during tissue culture and vegetative propagation, potentially affecting various traits in horticultural crops, but their characteristics are still unclear. Here, somatic mutations in regenerated woodland strawberry derived from tissue culture of shoot tips under different conditions and 12 cultivated strawberry individuals are analyzed by whole genome sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 × 10-8-3.0 × 10-6 mutations per site. CG methylation shows a stable reduction (0.71%-8.03%) in regenerated plants, and hypoCG-DMRs are more heritable after sexual reproduction. A high-quality haplotype-resolved genome is assembled for the strawberry cultivar "Beni hoppe." The 12 "Beni hoppe" individuals randomly selected from different locations show 4731-6005 mutations relative to the reference genome, and the mutation frequency varies among the subgenomes. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale and nucleotide resolution in plants.

Tribo-technological features of laser powder bed fusion process: scratch and wear resistance of AlSi10Mg aluminium alloy

Mechanical systems, regardless of their complexity, very often require that different parts must move relative to each other by sliding their surfaces, therefore appropriate tribological properties are needed. This request appears particularly evident for components fabricated through Metal Additive Manufacturing processes, due to their typical high surface roughness. In the current study, the Laser Powder Bed Fusion technique with optimized parameters is used to produce samples made of AlSi10Mg alloy. Their tribo-technological properties are investigated through progressive load scratch and dry ball-on-plate wear tests. Along with a global characterization, a local analysis has been performed to identify any variations induced by the building direction. The friction coefficient and the wear rate are generally higher than as-cast specimens. Finally, local trends suggest that the central parts of the samples average offer higher resistance to wear and scratch than the outer areas.

Assessment of local mechanical properties of laser powder bed fused aluminium alloy by non-destructive testing based on FIMEC indentation

Laser powder bed fusion process is a versatile metal additive manufacturing process. Although significant progress has been made so far, there is still limited large-scale adoption of this technique by the industry. The main problems are repeatability and lack of proper knowledge. In this work, an innovative and non-destructive testing methodology, based on flat-top cylinder indentation, was used to define the mechanical properties of laser powder bed fused aluminium alloy to highlight any variations induced by the combination of process parameters, for global characterization, and by the building direction, for local characterization. Results show similar or improved global mechanical properties of the laser powder bed fused specimens when compared to traditional die-casted ones. Indentation tests highlight a local dependence of properties along the building direction in favor of the upper part of the samples.

Global characterization of modelled micronekton in biophysically defined provinces

Micronekton are the mid-trophic level of the ecosystem and contribute to active carbon export to the deep ocean through diel vertical migrations. Better characterization of micronekton functional groups depending on relationships to environmental variables is useful for the management of marine resources, the conservation of biodiversity and a better understanding of climate change impacts. For this purpose, regionalization of global ocean into homogeneous provinces is an approach that is generating increasing interest. However, published regionalizations efforts (i) derived from environmental forcings, that do not specifically focus on micronekton and (ii) derived from acoustic backscatter, which do not allow direct estimates of micronekton biomass. Here, we propose to fill the gap between biophysical regionalizations and micronekton biomass. We notably defined biophysical biomes using global environmental variables known to affect micronekton: temperature of the epipelagic layer, temperature stratification, and net primary production (NPP). Six biophysical biomes were defined with a clustering method. A characterization of these biophysical biomes with simulated micronekton from the SEAPODYM-LMTL model displayed biome-specific relationships between biomass and the environmental variables used in the clustering (i.e. biomasses mostly structured by NPP and temperature). Biophysical biomes also displayed specific vertical structures suggested by modelled micronekton functional groups ratios. Then, a validation of biophysical biomes’ boundaries was performed to identify potential vertical structure reorganization in acoustic backscattering response from adjacent biomes. The regionalization identified homogeneous areas in terms of acoustic vertical structure, which were also different between adjacent biomes. Finally, a comparison with another biomes’ definition computed from micronekton biomasses suggested that environmental variables can account for only some of the variability of the micronekton structures.

Extrachromosomal circular DNAs in prostate adenocarcinoma: global characterizations and a novel prediction model.

The role of focal amplifications and extrachromosomal circular DNA (eccDNA) is still uncertain in prostate adenocarcinoma (PRAD). Here, we first mapped the global characterizations of eccDNA and then investigate the characterization of eccDNA-amplified key differentially expressed encoded genes (eKDEGs) in the progression, immune response and immunotherapy of PRAD. Circular_seq was used in conjunction with the TCGA-PRAD transcriptome dataset to sequence, annotate, and filter for eccDNA-amplified differentially expressed coding genes (eDEGs) in PRAD and para-cancerous normal prostate tissues. Afterwards, risk models were created and eKDEGs linked to the PRAD prognosis were identified using Cox and Lasso regression analysis. The immune microenvironment of the risk model was quantified using a variety of immunological algorithms, which also identified its characteristics with regard to immunotherapy, immune response, and immune infiltration. In this research, there was no significant difference in the size, type, and chromosomal distribution of eccDNA in PRAD and para-cancerous normal prostate tissues. However, 4,290 differentially expressed eccDNAs were identified and 1,981 coding genes were amplified. Following that, 499 eDEGs were tested in conjunction with the transcriptome dataset from TCGA-PRAD. By using Cox and Lasso regression techniques, ZNF330 and PITPNM3 were identified as eKDEGs of PRAD, and a new PRAD risk model was conducted based on this. Survival analysis showed that the high-risk group of this model was associated with poor prognosis and validated in external data. Immune infiltration analysis showed that the model risks affected immune cell infiltration in PRAD, not only mediating changes in immune cell function, but also correlating with immunophenotyping. Furthermore, the high-risk group was negatively associated with anti-CTLA-4/anti-PD-1 response and mutational burden. In addition, Tumor Immune Dysfunction and Exclusion analyses showed that high-risk group was more prone to immune escape. Drug sensitivity analyses identified 10 drugs, which were instructive for PRAD treatment. ZNF330 and PITPNM are the eKDEGs for PRAD, which can be used as potential new prognostic markers. The two-factor combined risk model can effectively assess the survival and prognosis of PRAD patients, but also can predict the different responses of immunotherapy to PRAD patients, which may provide new ideas for PRAD immunotherapy.

Radiogenomics: bridging the gap between imaging and genomics for precision oncology.

Genomics allows the tracing of origin and evolution of cancer at molecular scale and underpin modern cancer diagnosis and treatment systems. Yet, molecular biomarker-guided clinical decision-making encounters major challenges in the realm of individualized medicine, consisting of the invasiveness of procedures and the sampling errors due to high tumor heterogeneity. By contrast, medical imaging enables noninvasive and global characterization of tumors at a low cost. In recent years, radiomics has overcomes the limitations of human visual evaluation by high-throughput quantitative analysis, enabling the comprehensive utilization of the vast amount of information underlying radiological images. The cross-scale integration of radiomics and genomics (hereafter radiogenomics) has the enormous potential to enhance cancer decoding and act as a catalyst for digital precision medicine. Herein, we provide a comprehensive overview of the current framework and potential clinical applications of radiogenomics in patient care. We also highlight recent research advances to illustrate how radiogenomics can address common clinical problems in solid tumors such as breast cancer, lung cancer, and glioma. Finally, we analyze existing literature to outline challenges and propose solutions, while also identifying future research pathways. We believe that the perspectives shared in this survey will provide a valuable guide for researchers in the realm of radiogenomics aiming to advance precision oncology.

Fragmentation characterization in the circular restricted three body problem for cislunar space domain awareness

With heightened international interest in spacecraft activities in the vicinity of the Moon, cislunar space debris is likely to follow. Even one fragmentation event can have catastrophic and far-reaching consequences, which drives the need for appropriate debris characterization tools. How a single fragmentation plays out is highly dependent on any given initial condition in the near-chaotic cislunar region. This paper offers a means of structuring the cislunar region in terms of dynamical flow, which enables global characterization of fragmentation events without propagation of every possible case. This work investigates patterns in fragment behaviour as a function of energy, Δv, and orbit location, and explores emergent dynamic structures in the vicinity of the Earth-Moon L2 Lagrange point. Subsequent findings are applied to analysis of a realistic breakup event for a 500 kg satellite on an L2 Lyapunov orbit with a Jacobi constant of 3.0165, modeled using an in–house modified version of the NASA Standard Breakup Model.

Study on the global and nano-scale characterization of heat-induced changes in ordinary Portland cement paste

Cement-based composite materials can be damaged by distributed micro-cracking and degradation of hydration products when exposed to sustained high temperatures. In this study, a nano-scale characterization tool (dynamic nanoindentation) and global mechanical methods (vibration resonance frequency and damping) are employed to better understand the degradation of ordinary Portland cement paste subjected to high temperature exposures. A connection between the methods is demonstrated.

Global Characterization of DNA Methylation during Rice Leaf Angle Development.

During plant development and growth, genomic DNA accumulates chemical markers that determine the levels of gene expression. DNA methylation is an important epigenetic marker involved in plant developmental events. However, the characterization of the role of DNA methylation in rice leaf angle development has lagged behind. Herein, we performed bisulfite sequencing to characterize DNA methylation sites and performed transcriptome and small RNA sequencing during leaf angle development. The results revealed a global reduction in CG methylation during leaf angle establishment. A reduction in gene body CG methylation appears to play a vital role in leaf angle development. The hypomethylated and weakly expressed genes were functionally enriched in the brassinosteroid and auxin signaling pathways. Additionally, the main DNA methyltransferases were inactive. The addition of exogenous DNA methylation inhibitor 5-azacytidine increased the leaf angle, which confirmed that DNA methylation is crucial for leaf angle development. This study revealed a gradual decrease in 24-nucleotide siRNA levels during leaf angle development, particularly in relation to the enrichment of 24-nucleotide siRNAs at different hypomethylated regions that induce leaf angle inclination. Our results indicate crucial roles for DNA methylation in the rice leaf angle developmental stages.

Rapid discrimination between deleterious and benign missense mutations in the CAGI 6 experiment

We describe the machine learning tool that we applied in the CAGI 6 experiment to predict whether single residue mutations in proteins are deleterious or benign. This tool was trained using only single sequences, i.e., without multiple sequence alignments or structural information. Instead, we used global characterizations of the protein sequence. Training and testing data for human gene mutations was obtained from ClinVar (ncbi.nlm.nih.gov/pub/ClinVar/), and for non-human gene mutations from Uniprot (www.uniprot.org). Testing was done on post-training data from ClinVar. This testing yielded high AUC and Matthews correlation coefficient (MCC) for well trained examples but low generalizability. For genes with either sparse or unbalanced training data, the prediction accuracy is poor. The resulting prediction server is available online at http://www.mamiris.com/Shoni.cagi6.

A Chemoenzymatic Method Enables Global Enrichment and Characterization of Protein Arginine Methylation.

Arginine methylation is one of the most important post-translational modifications involved in the regulation of numerous biological processes. To better understand the biological significance of arginine methylation, enrichment methods need to be developed to analyze the methylated proteome at large-scale. Unfortunately, the prevailing enrichment method based on immunoaffinity purification can only enrich a subset of them due to the lack of pan-specific antibodies. Therefore, it is crucial to develop a stable and efficient antibody-free approach for the global analysis of arginine methylation. In this study, we developed a chemoenzymatic method for the simultaneous identification of mono- and dimethylated arginine. Totally, we identified 1006 arginine methylation events in Jurkat T cells, corresponding to 645 dimethylated sites and 361 monomethylated sites. We further applied the developed approach to global identification of the substrate proteins regulated by type I protein arginine methyltransferases (PRMTs) and identified 49 substrate proteins of type I PRMTs, which will facilitate a better understanding of PRMTs-regulated biological processes. Given the robust performance of this method, it would have broad application in methylproteomics analysis.

Biosynthetic pathway analysis combined with feature-based molecular networking to comprehensively characterize the chemical constituents in seeds of Sterculia lychnophora.

The seeds of Sterculia lychnophora Hance, commonly known as Pangdahai (PDH) in Chinese, have found extensive use in both culinary and traditional medicinal practices. However, a comprehensive understanding of the chemical composition of PDH has been lacking. This study proposes a strategy that integrates biosynthetic pathway analysis with feature-based molecular networking (FBMN), aiming for a thorough and global characterization of the chemical compositions of PDH. The FBMN map reveals potential compounds with structural similarity, and the MS/MS fragments could be annotated based on library matches, which could predict the plausible biosynthetic pathways in PDH, accomplishing the annotation of compounds clustered in FBMN by integrating biosynthetic pathways. Consequently, 126 compounds were plausibly or unambiguously identified, including 37 phenolic acids and glycosides, 20 flavonoids and glycosides, 12 procyanidins, 21 alkaloids, 22 lipids, and 14 others. Leveraging the information, 40 compounds, including 1 unique isoquinoline alkaloid and 2 rare linear furocoumarins, were isolated and confirmed. This study not only demonstrates a highly effective approach for identifying compounds within complex herbal mixtures but also establishes a robust foundation for the further development of PDH.

Usefulness of the 1H NMR Multisuppression Approach for the Global Characterization of Monovarietal Extra-Virgin Olive Oils.

Extra-virgin olive oil (EVOO) is one of the most appreciated vegetable oils worldwide, but its high price makes it prone to suffer adulteration with lower quality oils. Therefore, it is important to have methodologies able to study EVOO composition as a whole in a simple and fast way, in order to guarantee its quality and safety. For this purpose, in this study, commercial samples of five Spanish olive cultivars (Arbequina, Arroniz, Cornicabra, Hojiblanca, Picual) were studied by Proton Nuclear Magnetic Resonance (1H NMR) spectroscopy, using standard and multisuppression pulses. The aim was to explore the possibility of 1H NMR use to characterize in a single run and in a global way the composition of these monocultivar oils, regarding not only their main components (fatty acids supported on triglycerides) but also minor ones (squalene, sterols, diterpenic wax esters of phytol and geranylgeraniol, phenolic and secoiridoid derivatives, like tyrosol, hydroxytyrosol, oleacein, oleocanthal, and lignans, among others, and aldehydes). The use of univariate and multivariate statistical analyses confirmed the presence of compositional features that were specific to some olive varieties. The Arbequina and Arroniz oils showed the most characteristic features that allowed for clearly differentiating them from the others. In contrast, the discrimination between the Cornicabra, Hojiblanca and Picual oils was not so easily achieved.

Assessing chemical composition variations on vintage, vineyard location and grape ripeness: A regional study of red wines produced in the colorado river middle basin, La Pampa (Argentina)

This work aimed to characterize chemical composition of Malbec and Cabernet Franc red wines from two different regions of La Pampa’s province, which stands out as one of the youngest wine-producing regions in Argentina and has remained unexplored until now. These wines were produced from grapes of two consecutive vintages (2021 and 2022), and were harvested at two different ripeness levels. Global phenolic parameters, colour characterization and multi-elemental profile were evaluated. Multivariate statistical approaches were successfully implemented to investigate the vintage and ripeness effects on chemical profile of red wines and characterize them based on regional variations. Our results showed that vintage and ripeness affected both phenolic and multi-elemental profiles, and such chemical variables allowed the wines differentiation according to region. The results of this first study could form the basis for future research into optimizing the region’s winemaking potential.

The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L

BackgroundTheobroma cacao, the cocoa tree, is a tropical crop grown for its highly valuable cocoa solids and fat which are the basis of a 200-billion-dollar annual chocolate industry. However, the long generation time and difficulties associated with breeding a tropical tree crop have limited the progress of breeders to develop high-yielding disease-resistant varieties. Development of marker-assisted breeding methods for cacao requires discovery of genomic regions and specific alleles of genes encoding important traits of interest. To accelerate gene discovery, we developed a gene atlas composed of a large dataset of replicated transcriptomes with the long-term goal of progressing breeding towards developing high-yielding elite varieties of cacao.ResultsWe describe the creation of the Cacao Transcriptome Atlas, its global characterization and define sets of genes co-regulated in highly organ- and temporally-specific manners. RNAs were extracted and transcriptomes sequenced from 123 different tissues and stages of development representing major organs and developmental stages of the cacao lifecycle. In addition, several experimental treatments and time courses were performed to measure gene expression in tissues responding to biotic and abiotic stressors. Samples were collected in replicates (3–5) to enable statistical analysis of gene expression levels for a total of 390 transcriptomes. To promote wide use of these data, all raw sequencing data, expression read mapping matrices, scripts, and other information used to create the resource are freely available online. We verified our atlas by analyzing the expression of genes with known functions and expression patterns in Arabidopsis (ACT7, LEA19, AGL16, TIP13, LHY, MYB2) and found their expression profiles to be generally similar between both species. We also successfully identified tissue-specific genes at two thresholds in many tissue types represented and a set of genes highly conserved across all tissues.ConclusionThe Cacao Gene Atlas consists of a gene expression browser with graphical user interface and open access to raw sequencing data files as well as the unnormalized and CPM normalized read count data mapped to several cacao genomes. The gene atlas is a publicly available resource to allow rapid mining of cacao gene expression profiles. We hope this resource will be used to help accelerate the discovery of important genes for key cacao traits such as disease resistance and contribute to the breeding of elite varieties to help farmers increase yields.

Effect of TPMS reinforcement on the mechanical properties of aluminium–alumina interpenetrating phase composites

AbstractTriply Periodic Minimal Surface (TPMS)-based aluminium–alumina Interpenetrating Phase Composites (IPCs) manufactured through the combination of Additive Manufacturing (AM) and investment casting are explored in this study. Multiple alumina TPMS structures (Gyroid, Diamond, and Primitive) with different geometries and volume fractions were designed and fabricated using Digital Light Processing (DLP) AM technology. Afterwards, these ceramic structures were filled with an aluminium alloy via investment casting, uncovering an aluminium–alumina IPCs. A global characterization was performed, including ceramics shrinkage and mass loss; specimens’ morphology; chemical and crystalline characterization; density analysis and mechanical testing. Overall, DLP technology was found effective for producing these highly complex ceramic structures, with high surface quality. The sintered alumina structures presented a relative density of ca. 76.3% and a pseudo-ductile layer-by-layer failure behaviour, with Diamond-based TPMS exhibiting the highest compressive strength. Regarding the IPCs, the addition of aluminium significantly changed the compressive behaviour of the samples, presenting an energy absorption behaviour. The integration of the alumina phase into the aluminium alloy led to an improvement on the compressive offset stress of approximately 6% when compared to the aluminium alloy used. Diamond and Gyroid IPCs demonstrated similar mechanical behaviour and the highest mechanical performance. Graphical Abstract

Global characterization of a laser-generated neutron source

Laser-driven neutron sources are routinely produced by the interaction of laser-accelerated protons with a converter. They present complementary characteristics to those of conventional accelerator-based neutron sources (e.g. short pulse durations, enabling novel applications like radiography). We present here results from an experiment aimed at performing a global characterization of the neutrons produced using the Titan laser at the Jupiter Laser Facility (Livermore, USA), where protons were accelerated from 23 $\mathrm {\mu }$ m thick plastic targets and directed onto a LiF converter to produce neutrons. For this purpose, several diagnostics were used to measure these neutron emissions, such as CR-39, activation foils, time-of-flight detectors and direct measurement of $^7{\rm Be}$ residual activity in the LiF converters. The use of these different, independently operating diagnostics enables comparison of the various measurements performed to provide a robust characterization. These measurements led to a neutron yield of $2.0\times 10^{9}$ neutrons per shot with a modest angular dependence, close to that simulated.

A freeway vehicle early warning method based on risk map: Enhancing traffic safety through global perspective characterization of driving risk

In the era of rapid advancements in intelligent transportation, utilizing vehicle operating data to evaluate the risk of freeway vehicles and study on vehicle early warning methods not only lays a theoretical foundation for improving the active safety of vehicles, but also provides the technical support for reducing accident rate. This paper proposes a freeway vehicle early warning method based on risk map to enhance vehicle safety. Firstly, Modified Time-to-Collision (MTTC), a two-dimensional indicator that describes the risk of inter-vehicle travel, is used as an indicator of road traffic risk. This paper designs a transformation function to probabilistically transform MTTC into Risk Indicators (RI). The single-vehicle risk map is generated based on the mapping relationship between the risk values and the corresponding roadway segments. These single-vehicle risk maps of all vehicles on the road are superimposed to construct the risk map, which is used to describe the risk distribution in the freeway. Then, a vehicle early warning framework is built based on the risk map. The risk values in the risk map are compared with predefined early warning thresholds to alert the vehicle when it enters a high-risk state. Finally, VISSIM is used to carry out simulation experiments. The experiment simulates a freeway accident stopping situation. This scenario includes sub-scenarios such as unplanned stopping and lane-changing, continuous lane-changing, and adjacent lane overtaking. We analyze the risk map and vehicle warning results in different sub-scenarios, evaluate the risk changes of the vehicles before and after receiving the warning, and compare the warning results of the method in this paper with other alternative methods. The method is applied to 17 vehicles in the simulation to adjust their motion states. The results show that the total warning time is reduced by 29.6% and 73.3% of vehicles change lanes away from the accident vehicle. The overall results validate the effectiveness of the vehicle early warning method based on risk map proposed in this paper.