Structural Variations Research Articles

Temporal dynamics of parasite populations and communities of blue sea catfish Ariopsis guatemalensis (Günther, 1864), in a eutrophic coastal lagoon from Mexican Pacific

ABSTRACT The temporal dynamics of parasite populations and communities of blue sea catfish Ariopsis guatemalensis from a tropical eutrophic coastal lagoon was studied during an annual cycle. A total of 620 adult fishes were collected between January and December 2019. Eleven taxa of parasites were identified, three of monoxenous (single-host life cycle), and eight of heteroxenous (multi-host life cycle) parasites. The infection levels of two monoxenous (Neotetraonchus vegrandis and Ergasilus sp.) and five heteroxenous (Austrodiplostomum sp. Pseudoacanthostomum panamense, Pseudoleptorhynchoides lamothei, Contracaecum sp. and Hysterothylacium perezi) parasite species varied between sampling months and/or climatic seasons. The infection dynamics of these group of parasites were influenced by environmental changes generated by the dry/rainy cycle, which can affect the availability of intermediate host populations, and the feeding and reproductive behaviour of the host. Although the species composition of the parasite communities remains quite stable over time, its structure registers important changes mainly during the rainy season. Some host traits such as the feeding and reproductive behaviour, body size, physical condition, and sex of the host, as well as the temporal replacement of numerically dominant parasite species, were the main factors responsible for variations in the parasite community structure.

Visual working memory models of delayed estimation do not generalize to whole-report tasks.

Whole-report working memory tasks provide a measure of recall for all stimuli in a trial and afford single-trial analyses that are not possible with single-report delayed estimation tasks. However, most whole-report studies assume that trial stimuli are encoded and reported independently, and they do not consider the relationships between stimuli presented and reported within the same trial. Here, we present the results of two independently conducted whole-report experiments. The first dataset was recorded by Adam, Vogel, and Awh (2017) and required participants to report color and orientation stimuli using a continuous response wheel. We recorded the second dataset, which required participants to report color stimuli using a set of discrete buttons. We found that participants often group their reports by color similarity, contradicting the assumption of independence implicit in most encoding models of working memory. Next, we showed that this behavior was consistent across participants and experiments when reporting color but not orientation, two circular variables often assumed to be equivalent.Finally, we implemented an alternative to independent encoding where stimuli are encoded as a hierarchical Bayesian ensemble and found that this model predicts biases that are not present in either dataset. Our results suggest that assumptions made by both independent and hierarchical ensemble encoding models-which were developed in the context of single-report delayed estimation tasks-do not hold for the whole-report task. This failure to generalize highlights the need to consider variations in task structure when inferring fundamental principles of visual working memory.

Revealing the structural variation and degradation mechanism of cellulose during ozone oxidation treatment

Despite numerous studies on the use of ozone for the removal of non-cellulosic substances from lignocellulosic fibers, the mechanism underlying cellulose degradation and the oxidized group formation during ozone oxidation treatment remain unclear. This study focuses on the extraction of α-cellulose from flax fibers. The effect of ozone oxidation on the degree of polymerization (DP) and oxidized groups in α-cellulose under different operational conditions (ozone concentration, oxidation time, water pick-up value, initial pH value) were thoroughly investigated. Additionally, the quality of α-cellulose oxidized under different phases (gas and liquid) of ozone reaction was systematically compared. Results showed that the DP value of α-cellulose-O3-Gas-80% (130 mg·L−1·min−1, 15 min, WPV 80%, pH 2.0) was lower than that of α-cellulose-O3-Liquid (130 mg·L−1·min−1, 15 min, 1:30 g·mL−1, pH 2.0) and α-cellulose-O3-Gas-0% (130 mg·L−1·min−1, 15 min). However, the carboxyl and carbonyl contents showed the opposite trends. FTIR results showed a new peak (carboxyl peak) for α-cellulose and a reduction of hydrogen bonding interactions in molecules after ozone oxidation. In addition, the crystallinity and thermal stability of α-cellulose decreased after ozone oxidation, with α-cellulose-O3-Gas-80% exhibiting the most significant decline. SEM analysis showed that the morphology of α-cellulose was changed after ozone oxidation. This study provides some guidance to mitigate ineffective degradation of cellulose and assist in the selection of cellulose protectors during the process of extracting lignocellulosic fibers by ozone oxidation.

On the Layered Structure and Seasonal Variation of the Water Exchanges in the Sulawesi Sea Areas As Well As the Associated Dynamics

AbstractThe layered structure and seasonal variation of the water exchanges in the Sulawesi Sea areas, as well as the corresponding dynamics, are investigated using HYCOM data. A net inward water mass transport is identified in the upper and intermediate layers in the Sulawesi Sea and it is compensated by the net outward transport in the deep layer. As an important source of this net inward transport, the southward flow through the Sibutu Passage (denoted hereafter as Sibutu Flow) reaches 5.06 Sv in winter, accounting for ∼43% of the net inflow. However, it decreases substantially to 1.79 Sv in summer, accounting for only 12% of the inflow. Further analysis reveals that this Sibutu Flow modulates the seasonal variation of the corresponding outward flow at the Makassar Strait, the major exit of the water mass in the Sulawesi Sea. In winter, the enhancement of the Sibutu Flow associated with the greater intrusion of Kuroshio water into the Luzon Strait produces a stronger eastward pressure gradient force, suppressing the surface intrusion of the Mindanao Current. Conversely, this pressure gradient force weakens and shifts westward in summer, permitting a larger water intrusion from the eastern section. Given that the outward Makassar Flow is the main passage of the Indonesian Throughflow (ITF), our study highlights the essential role of the Sibutu Flow in modulating seasonal variabilities of the ITF via the Makassar Strait and, thus, the transfer of water masses and heat content between the Pacific and Indian Oceans.

Structural and performance variations of aluminoborosilicate glass substrates with mixed alkaline earth effect for applications in 3D integrated packaging

Alkali-free aluminoborosilicate glass substrates possess excellent chemical stability and outstanding thermodynamic and dielectric properties, rendering them promising candidates for applications in three-dimensional integrated packaging. This study investigates the structural and performance variations in RO (RBa,Sr)–Al2O3–B2O3–SiO2 glass substrates with a mixed alkaline earth effect under different BaO/SrO ratios (with a constant RO value of 20 mol%). The glass substrates were analyzed using various methods, including X-ray diffraction, differential scanning calorimetry, coefficient of thermal expansion, Raman spectroscopy, and 1 MHz–1 GHz dielectric property tests. Raman spectroscopy was used to measure the glass network connectivity using R12/34 (degree of [SiO4] units depolymerization) and N4 (degree of [BO4] units polymerization). The results show that the RABS15 sample had a significant reduction in dielectric loss at a frequency of 1 GHz compared with the other glass samples, corresponding to the best glass network connectivity. The main cause of high-frequency dielectric loss was the presence of [BO3] units in the glass network. During the preparation process, it was discovered that placing the crucible with mixed raw materials in an elevator-type furnace at a high temperature is an effective measure for solving the crystallization problem.

Structural Variation Along the Southern Hikurangi Subduction Zone, Aotearoa New Zealand, From Seismic Reflection and Retro‐Deformation Analysis

AbstractThe southern Hikurangi subduction zone exhibits significant along‐strike variation in convergence rate and obliquity, sediment thickness and, uniquely, the increasing proximity of southern Hikurangi to, and impingement on, the incoming continental Chatham Rise, an ancient Gondwana accretionary complex. There are corresponding changes in the morphology and structure of the Hikurangi accretionary prism. We combine widely spaced multichannel seismic reflection profiles with high resolution bathymetry and previous interpretations to characterize the structure and the history of the accretionary prism since 2 Ma. The southern Hikurangi margin can be divided into three segments. A northeastern segment (A) characterized by a moderately wide (∼70 km), low taper (∼5°) prism recording uninhibited outward growth in the last ∼1 Myr. Deformation resolvable in seismic reflection data accounts for ∼20 % of plate convergence, comparable with the central Hikurangi margin further North. A central segment (B) characterized by a narrow (∼30 km), moderate taper (∼8°) prism, with earlier (∼2‐∼1 Ma) shortening than segment A. Outward prism growth ceased coincidentally with development of major strike‐slip faults in the prism interior, reduced margin‐normal convergence rate, and the onset of impingement on the incoming Chatham Rise to the south. A southwestern segment (C) marks the approximate southern termination of subduction but widens to ∼50 km due to rapid outward migration of the deformation front via fault reactivation within the now‐underthrusting corner of the Chatham Rise. Segment C exhibits minimal shortening as margin‐normal subduction velocity decreases and plate motion is increasingly taken up by interior thrusts and strike‐slip faults.

Buoyancy glitches in pulsating stars revisited

Sharp structural variations induce specific signatures on stellar pulsations that can be studied to infer localised information on the stratification of the star. This information is key to improve our understanding of the physical processes that lead to the structural variations and how to model them. Here we revisit and extend the analysis of the signature of different types of buoyancy glitches in gravity-mode and mixed-mode pulsators presented in earlier works, including glitches with step-like, Gaussian-like, and Dirac-δ-like shapes. In particular, we provide analytical expressions for the perturbations to the periods and show that these can be reliably used in place of the expressions provided for the period spacings, with the advantage that the use of the new expressions does not require modes with consecutive radial orders to be observed. Based on a comparison with two limit cases and on simulated data, we further tested the accuracy of the expression for the Gaussian-like glitch signature whose derivation in an earlier work involved a significant approximation. We find that the least reliable glitch parameter inferred from fitting that expression is the amplitude, which can be up to a factor of two larger than the true amplitude, reaching this limit when the glitch is small. We further discuss the impact on the glitch signature of considering a glitch in the inner and outer half of the g-mode cavity, emphasising the break of symmetry that takes place in the case of mixed-mode pulsators.

Haplotype-resolved assembly of the mule duck genome using high-fidelity sequencing technology.

Mule duck is vitally important to the production of global duck meat. Here, we present two high-quality haplotypes of a female mule duck (haplotype 1 (H1):1.28 Gb, haplotype 2 (H2): 1.40 Gb). The continuity (H1: contig N50 = 14.90 Mb, H2: contig N50 = 15.70 Mb) and completeness (BUSCO: H1 = 96.9%, H2 = 97.3%) are substantially better than those of other duck genomes. We detected the structural variations (SVs) in H1 and H2. We observed a positive correlation between autosome length and the number of SVs. Z chromosome was some deficient in deletions and insertions, but W chromosome was some excessive. A total of 1,451 genes were haplotype specific expression (HSEs). Among them, 737 specifically expressed in H1, and 714 specifically expressed in H2. We found that H1 and H2 HSEs tended to be involved in similar biological processes, such as myometrial relaxation and contraction pathways, muscle structure development and phosphorylation. Our haplotype-resolved genome assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in mule duck.

Injection-induced basement seismicity beneath the Raton Basin: constraints from refined fault architectures and basin structure.

Intraplate earthquakes induced by anthropogenic fluid injection present unexpected seismic risk to previously quiescent or low seismicity-rate regions. Despite many studies of induced seismicity, there are relatively few with detailed openly accessible constraints on the interaction between seismic sources and subsurface structures. In this study of the Raton Basin, we refine source observations from a dense nodal array and constrain basin structure using teleseismic receiver functions. The cross-correlation-based relocated hypocentres and a new set of focal mechanisms light up active fault segments and show clear spatiotemporal patterns. The geometric complexity of reactivated fault clusters appears greatest near higher rate injection wells. Simpler normal fault structure is found farther from injection wells and near abrupt structural transitions suggested by receiver functions. While less induced seismicity in the crystalline basement is expected when injection is >1 km from the top of the basement (like Raton), our receiver function analysis identified a basin thickness ~3 km beneath the nodal array and lateral variations in sedimentary structures. Our results explain potential fluid connectivity between the injection depths focused at ~1-1.5 km below the surface and basement fault activity that begins at ~3 km and reaches peak activity at ~4-8 km depths. This article is part of the theme issue 'Induced seismicity in coupled subsurface systems'.

Drivers of public procurement prices: Evidence from pharmaceutical markets

This paper examines the determinants of public procurement prices using comprehensive data on pharmaceutical purchases by the public sector in Chile. We first document sizable price differences between buyers for the same product and quantity purchased: the difference between the average prices paid by buyers at the 90th and 10th percentiles of the distribution is 16 percent. Our main results are related to the importance of market structure in explaining the dispersion in procurement prices. We find that market structure explains three times more dispersion than buyer effects. Moreover, we leverage exogenous variation in market structure due to patent expirations to estimate that the entry of an additional seller decreases average procurement prices by 11.7 percent, which is 72 percent of the price differences implied by the gap between the 90th and 10th percentiles of estimated buyer effects. These results suggest that supply-side factors are relevant determinants of public procurement prices and that their quantitative importance may exceed that of demand-side factors previously emphasized in the literature.

Habitat structural complexity predicts cognitive performance and behaviour inwestern mosquitofish.

Urban stream syndrome alters stream habitat complexity. We define habitat complexity as the degree of variation in physical habitat structure, with increasing variation equating to higher complexity. Habitat complexity affects species composition and shapes animal ecology, physiology, behaviour and cognition. We used a delayed detour test to measure whether cognitive processes (motor self-regulation) and behaviour (risk-taking) of female Western mosquitofish, Gambusia affinis, varied with habitat structural complexity (low, moderate and high) that was quantified visually for nine populations. We predicted that motor self-regulation and risk-taking behaviour would increase with increasing habitat complexity, yet we found support for the opposite. Lower complexity habitats offer less refuge potentially leading to higher predation pressure and selecting for greater risk-taking by fish with higher motor self-regulation. Our findings provide insight into how habitat complexity can shape cognitive processes and behaviour and offers a broader understanding of why some species may tolerate conditions of urbanized environments.

Ant social network structure is highly conserved across species.

The ecological success of social insects makes their colony organization fascinating to scientists studying collective systems. In recent years, the combination of automated behavioural tracking and social network analysis has deepened our understanding of many aspects of colony organization. However, because studies have typically worked with single species, we know little about interspecific variation in network structure. Here, we conduct a comparative network analysis across five ant species from five subfamilies, separated by more than 100 Myr of evolution. We find that social network structure is highly conserved across subfamilies. All species studied form modular networks, with two social communities, a similar distribution of individuals between the two communities, and equivalent mapping of task performance onto the communities. Against this backdrop of organizational similarity, queens of the different species occupied qualitatively distinct network positions. The deep conservation of the two community structure implies that the most fundamental behavioural division of labour in social insects is between workers that stay in the nest to rear brood, and those that leave the nest to forage. This division has parallels across the animal kingdom in systems of biparental care and probably represents the most readily evolvable form of behavioural division of labour.

Leakage current control of Y-HfO2 for dynamic random access memory applications via ZrO2 stacking

Pristine HfO2 tends to have a monoclinic phase with a low dielectric constant. Reportedly, yttrium(Y) doping has been used to induce the tetragonal phase in HfO2, with Y contributing to the formation of the tetragonal phase and improving the crystallinity. However, Y doping in HfO2 forms oxygen vacancies, resulting in a relatively high leakage current. Owing to the difficulty in suppressing the oxygen vacancies crucial for inducing the tetragonal phase, we focused on another significant leakage current path: the grain boundary. Introducing a heterostructure is expected to reduce the grain size and mitigate the leakage current by increasing the length of the leakage path. This study compares the dielectric constant and leakage current based on the stacking sequence of ZrO2 and Y-doped HfO2 (Y-HfO2) and elucidate the underlying differences through electrical analysis. Additionally, crystallographic analysis reveals the reasons for the structural order-dependent variations in the electrical properties. Finally, the structure with a Y-HfO2 layer at the bottom demonstrates advantages in achieving a lower leakage current.

Melodia: A Python Library for Protein Structure Analysis.

Analysing protein structure similarities is an important step in protein engineering and drug discovery. Methodologies that are more advanced than simple RMSD are available but often require extensive mathematical or computational knowledge for implementation. Grouping and optimising such tools in an efficient open-source library increases accessibility and encourages the adoption of more advanced metrics. Melodia is a Python library with a complete set of components devised for describing, comparing and analysing the shape of protein structures using differential geometry of three-dimensional curves and knot theory. It can generate robust geometric descriptors for thousands of shapes in just a few minutes. Those descriptors are more sensitive to structural feature variation than RMSD deviation. Melodia also incorporates sequence structural annotation and three-dimensional visualisations. Melodia is an open-source Python library freely available on https://github.com/rwmontalvao/Melodia_py, along with interactive Jupyter Notebook tutorials. Supplementary data are available at Bioinformatics online.

Genomic Insights Into High-Grade Infarct-Associated Bone Sarcomas

Sarcomas rarely develop in bones previously compromised by infarcts. These infarct-associated sarcomas often present as undifferentiated pleomorphic sarcomas (UPS), and their genetic characteristics are poorly understood. High-grade UPS of bone are typically treated with a combination of surgery and chemotherapy, similar to osteosarcoma. We conducted a detailed clinicopathologic and genomic analysis of 6 cases of intraosseous sarcomas arising from histologically and radiographically confirmed bone infarcts. We analyzed 523 genes for sequence-level mutations using next-generation sequencing with the TruSight Oncology 500 panel and utilized whole-genome single nucleotide polymorphism Microarray (OncoScan CNV) to detect copy number alterations and loss of heterozygosity (LOH). Genomic instability was assessed through homologous recombination deficiency (HRD) metrics, incorporating LOH, telomeric allelic imbalance, and large-scale state transitions. Fluorescence in situ hybridization and immunohistochemistry validated the findings. The cohort included 3 men and 3 women, with a median age of 70 years, and tumors located in the femur and tibia. Five of the 6 patients developed distant metastases. Treatment involved surgery and chemotherapy or immune checkpoint inhibitors. Genomic analysis revealed significant complexity and high HRD scores, ranging from 32 to 57 (with a cutoff of 32). Chromosome 12 alterations, including segmental amplification or chromothripsis, were observed in 4 cases. Notably, MDM2 amplification, confirmed by fluorescence in situ hybridization, was detected in 2 cases. Homozygous deletion of CDKN2A/B was observed in all six cases. Tumor mutational burden levels ranged from 2.4 to 7.9 mutations per megabase. Notable pathogenic mutations included H3-3A mutations (p.G35R and p.G35W), and mutations in HRAS, DNMT3A, NF2, PIK3CA, POLE, and TP53, each in one case. These results suggest that high-grade infarct-associated sarcomas of bone, whereas sharing high levels of structural variations with osteosarcoma, may exhibit potentially less frequent TP53 mutations and more common CDKN2A/B deletions. This points to the possibility that the mutation spectrum and disrupted pathways could be distinct from conventional osteosarcoma.

Weld Defect Inspection of Cylindrical Secondary Batteries Based on Active Thermographic Measurement with Thermal Magnification

This paper presents an active thermographic measurement-based inspection tech-nique for detecting weld defects in the battery cap region of cylindrical secondary batteries. As the proliferation of electric vehicles continues, safety issues related to secondary batteries have become prominent. In this study, a defect detection algorithm was developed by aligning visual images and active thermographic im-ages of the cylindrical secondary battery cap region. Lock-in amplitude images during the heating-cooling process using a laser were extracted to measure the difference in temperature patterns arising from internal structural variations. Ad-ditionally, to minimize the influence of surface conditions and temperature varia-tions other than laser-induced, a 10Hz periodic heating was employed, and ther-mal magnification in the heating frequency was achieved through data processing. This approach allowed the measurement of temperature changes induced by laser heating and cooling while minimizing the impact of surface conditions and tem-perature variations unrelated to the laser. A dataset of 1000 specimens was con-structed by aligning thermographic data with vision images acquired through this method. defective samples. Using this thermographic-vision alignment dataset, a defect detection algorithm was trained to achieve a more accurate and faster in-spection performance compared to existing non-destructive testing technologies.

Relationships between the appearance quality and starch structure of soft rice under different nitrogen levels

AbstractThis study aims to explore the formation mechanism of starch structure and the relationships between the appearance quality and starch structure of soft rice under different nitrogen levels. We comprehensively investigated the physiological aspects, starch structure variations, and appearance quality of soft rice in response to different nitrogen applications. The results showed that under the moderate nitrogen application (270 N), the soft rice exhibited the highest AGPase activity, the highest large‐starch granule content, and the lowest chalkiness. Under the highest nitrogen application (360 N), the soft rice exhibited the highest GBSS and DBE activity and the lowest SBE activity, the highest content of long‐branched amylopectin, the lowest relative crystallinity, the fewest ordered structures, the most amorphous structures, the largest semi‐crystalline lamellar thicknesses, and the highest transparency of chalk‐free rice. In conclusion, moderate nitrogen fertilization (270 N) improved the AGPase activity, which leaded to fuller starch granules and more compact endosperm in soft rice. Thus, the grain chalkiness of soft rice decreased. Continuous nitrogen application (0‐360 N) constantly increased the GBSS and DBE activity and reduced the SBE activity in soft rice, leading a lower content of short‐branched amylopectin and a higher content of long‐branched amylopectin in soft rice. Thus, the relative crystallinity and ordered structures of soft rice were reduced. These structures improved the transparency phenotype of soft rice.

Detection of an 8p23.1 Inversion Using High-Resolution Optical Genome Mapping

Abstract Objective To evaluate the performance of optical genome mapping (OGM) in identifying an inversion located in the short arm of chromosome 8 (8p, 8p23.1), flanked by regions of complex segmental duplication (SD), using the GRCh38 and telomere-to-telomere (T2T) genome references. Methods We investigated a couple suspected of carrying the 8p23.1 inversion due to a terminal deletion combined with an interstitial duplication of 8p found in their abortus. OGM was performed on both individuals. The data were mapped to the current GRCh38 and the updated T2T genome references, respectively. Results The 8p23.1 inversion was observed in the female when mapping OGM data to the T2T assembly. In contrast, under the GRCh38 reference, the orientation between the suspected breakpoints within the SD regions could not be distinguished. Additional variants of uncertain significance were also identified in both individuals. Conclusion Our findings highlight the superiority of the T2T reference in recognizing structural variations involving SD regions. The enhanced SV detection using the T2T reference may contribute to a better understanding of genome instability and human diseases.

Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species

Understanding the ecological adaptation of tree species can not only reveal the evolutionary potential but also benefit biodiversity conservation under global climate change. Quercus is a keystone genus in Northern Hemisphere forests, and its wide distribution in diverse ecosystems and long evolutionary history make it an ideal model for studying the genomic basis of ecological adaptations. Here we used a newly sequenced genome of Quercus gilva, an evergreen oak species from East Asia, with 18 published Fagales genomes to determine how Fagaceae genomes have evolved, identify genomic footprints of ecological adaptability in oaks in general, as well as between evergreen and deciduous oaks. We found that oak species exhibited a higher degree of genomic conservation and stability, as indicated by the absence of large-scale chromosomal structural variations or additional whole-genome duplication events. In addition, we identified expansion and tandem repetitions within gene families that contribute to plant physical and chemical defense (e.g., cuticle biosynthesis and oxidosqualene cyclase genes), which may represent the foundation for the ecological adaptation of oak species. Circadian rhythm and hormone-related genes may regulate the habits of evergreen and deciduous oaks. This study provides a comprehensive perspective on the ecological adaptations of tree species based on phylogenetic, genome evolutionary, and functional genomic analyses.

A catalogue of recombination coldspots in interspecific tomato hybrids.

Increasing natural resistance and resilience in plants is key for ensuring food security within a changing climate. Breeders improve these traits by crossing cultivars with their wild relatives and introgressing specific alleles through meiotic recombination. However, some genomic regions are devoid of recombination especially in crosses between divergent genomes, limiting the combinations of desirable alleles. Here, we used pooled-pollen sequencing to build a map of recombinant and non-recombinant regions between tomato and five wild relatives commonly used for introgressive tomato breeding. We detected hybrid-specific recombination coldspots that underscore the role of structural variations in modifying recombination patterns and maintaining genetic linkage in interspecific crosses. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. About two-thirds of the genome are conserved coldspots, located mostly in the pericentromeres and enriched with retrotransposons. The coldspots also harbor genes associated with agronomic traits and stress resistance, revealing undesired consequences of linkage drag and possible barriers to breeding. We presented examples of linkage drag that can potentially be resolved by pairing tomato with other wild species. Overall, this catalogue will help breeders better understand crossover localization and make informed decisions on generating new tomato varieties.