Structural Variations Research Articles

V4RIN: visual analysis of regional industry network with domain knowledge.

The regional industry network (RIN) is a type of financial network derived from industry networks that possess the capability to describe the connections between specific industries within a particular region. For most investors and financial analysts lacking extensive experience, the decision-support information provided by industry networks may be too vague. Conversely, RINs express more detailed and specific industry connections both within and outside the region. As RIN analysis is domain-specific and current financial network analysis tools are designed for generalized analytical tasks and cannot be directly applied to RINs, new visual analysis approaches are needed to enhance information exploration efficiency. In this study, we collaborated with domain experts and proposed V4RIN, an interactive visualization analysis system that integrates predefined domain knowledge and data processing methods to support users in uploading custom data. Through multiple views in the system panel, users can comprehensively explore the structure, geographical distribution, and spatiotemporal variations of the RIN. Two case studies were conducted and a set of expert interviews with five domain experts to validate the usability and reliability of our system.

Effects of natural Ionones and derived novel analogues with simplified structures on behavioral responses of whiteflies.

Whiteflies are major pests in agriculture, causing damage to crops and transmitting plant viruses. Using Volatile Organic Compounds (VOCs) as semiochemicals offers a sustainable approach for combating whiteflies. One such group of compounds, represented by β-ionone, has been found to possess repellent/attractant properties. To further explore the behavioral effects of these compounds on whiteflies, we selected five natural ionone compounds and synthesized six novel analogues to examine the impact of structural variations on whitefly behavior. Our results demonstrated that β-ionone and its analogues have a significant impact on the behavior of whiteflies. Among them, 0.01% pseudo ionone solution exhibited an attractant effect on whiteflies. Notably, the application of 1% β-ionone and 0.1% β-ionol solution demonstrated a notable repellent effect and oviposition deterrent effect on whitefly. We also found that the novel ionone analogue (±)1A exhibited a strong repellent effect. Both β-ionol and compound (±)1A possess high logP values and low saturation vapor pressures, which contribute to enhanced lipophilicity, making them more likely to penetrate insect antennae and prolong their presence in the air. The newly discovered ionone analogue (±)1A and β-ionol exhibit improved repellent effects, while pseudo ionone shows an attractant effect. These three compounds hold promising potential for development as novel biological control agents. Our work highlights the efficacy of VOCs as a protection method against whiteflies. These findings indicate that our new technology for a 'push-pull' control method of B. tabaci can offer a novel tool for integrated pest management (IPM). © 2024 Society of Chemical Industry.

Organ- and Cell-Selective Delivery of mRNA In Vivo Using Guanidinylated Serinol Charge-Altering Releasable Transporters.

Selective RNA delivery is required for the broad implementation of RNA clinical applications, including prophylactic and therapeutic vaccinations, immunotherapies for cancer, and genome editing. Current polyanion delivery relies heavily on cationic amines, while cationic guanidinium systems have received limited attention due in part to their strong polyanion association, which impedes intracellular polyanion release. Here, we disclose a general solution to this problem in which cationic guanidinium groups are used to form stable RNA complexes upon formulation but at physiological pH undergo a novel charge-neutralization process, resulting in RNA release. This new delivery system consists of guanidinylated serinol moieties incorporated into a charge-altering releasable transporter (GSer-CARTs). Significantly, systematic variations in structure and formulation resulted in GSer-CARTs that exhibit highly selective mRNA delivery to the lung (∼97%) and spleen (∼98%) without targeting ligands. Illustrative of their breadth and translational potential, GSer-CARTs deliver circRNA, providing the basis for a cancer vaccination strategy, which in a murine model resulted in antigen-specific immune responses and effective suppression of established tumors.

Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

BackgroundBreast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non-luminal A tumors, classified as difficult-to-treat breast cancers (DTBC). This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors.MethodsWe retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired-end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and survival analysis were performed to better understand DTBC and investigate biomarkers.ResultsWe observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation-related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and proteomic analysis. Distinct DTBC and LumA-enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse-risk and low relapse-risk basal-like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors.ConclusionsThis study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.

Genomic analysis uncovers novel candidate genes related to adaptation to tropical climates and milk production traits in native goats

BackgroundSince domestication, both evolutionary forces and human selection have played crucial roles in producing adaptive and economic traits, resulting in animal breeds that have been selected for specific climates and different breeding goals. Pakistani goat breeds have acquired genomic adaptations to their native climate conditions, such as tropical and hot climates. In this study, using next-generation sequencing data, we aimed to assess the signatures of positive selection in three native Pakistani goats, known as milk production breeds, that have been well adapted to their local climate.ResultsTo explore the genomic relationship between studied goat populations and their population structure, whole genome sequence data from native goat populations in Pakistan (n = 26) was merged with available worldwide goat genomic data (n = 184), resulting in a total dataset of 210 individuals. The results showed a high genetic correlation between Pakistani goats and samples from North-East Asia. Across all populations analyzed, a higher linkage disequilibrium (LD) level (– 0.59) was found in the Pakistani goat group at a genomic distance of 1 Kb. Our findings from admixture analysis (K = 5 and K = 6) showed no evidence of shared genomic ancestry between Pakistani goats and other goat populations from Asia. The results from genomic selection analysis revealed several candidate genes related to adaptation to tropical/hot climates (such as; KITLG, HSPB9, HSP70, HSPA12B, and HSPA12B) and milk production related-traits (such as IGFBP3, LPL, LEPR, TSHR, and ACACA) in Pakistani native goat breeds.ConclusionsThe results from this study shed light on the structural variation in the DNA of the three native Pakistani goat breeds. Several candidate genes were discovered for adaptation to tropical/hot climates, immune responses, and milk production traits. The identified genes could be exploited in goat breeding programs to select efficient breeds for tropical/hot climate regions.

Study on the photodegradation behaviors of thermal-aged silk

In museums, silk cultural relics are highly sensitive to light. However, lighting is inevitable due to the exhibition needs, despite any light would pose irreversible damage to silk. Although the solution of eliminating UV radiation was widely achieved in museum lighting environment, long-time accumulation of other light sources still would induce photodegradation of silk. This work therefore established the simulated light ageing experiments to assess the degradation behaviors of silk samples with different ageing degrees. The variation of color values and structure transformation of each sample group were determined by the means of scanning electron microscopy (SEM), colorimeter, Fourier Transform infrared spectroscopy (FTIR) and 13C CPMAS NMR. The results indicated that silk samples with different initial ageing degrees presented different discoloration tendency and structural variation in experimental lighting environment, suggesting the higher disordered structure makes the silk more vulnerable to light damage. It is of great significance to understand the long-time impacts of illumination on degraded silk and further provide methodology for predicting the duration of exhibited silk cultural relics.

Enhancing CO2 Capture via Metal-Ligand Cooperativity: Tuning Ligand Basicity and Zn(II) Lewis Acidity.

A series of thiosemicarbazonato-hydrazinatopyridine zinc(II) complexes were evaluated as direct air CO2 capture agents. The complexes sequester CO2 in a methanol solution as a metal-coordinated methylcarbonate. The reaction is reversible upon sparging of solutions with an inert gas (N2 or Ar). The capture process involves metal-ligand cooperativity with the noncoordinating nitrogen of the hydrazinatopyridine functional group serving as a Brønsted-Lowry base and the zinc acting as a Lewis acid. In this study, the pendent amine of the thiosemicarbazonato group was varied to include 4-phenyl (ZnL5), 4-(trifluoromethyl)phenyl (ZnL6), 4-cyanophenyl (ZnL7), 4-tolyl (ZnL8), and 4-naphthyl (ZnL9). Hyperconjugation between the pendent group and the ligand core resulted in modulation of the metal ion acidity, as quantified by ligand exchange equilibrium constants (K3 = 193-511) and ligand basicity (pKa,MeOH = 11.09-11.94). Variations in electronic structure that decreased ligand basicity were more than offset by increases in Lewis acidity. The equilibrium constant (K1) for CO2 capture varied from 46300 to 73700. Overall, the value of K1 was directly related to the relative Lewis acidity of the complexes (K3). Notably, there was an overall inverse relationship between K1 and the ligand basicity. The results provide insights into ligand design to further improve CO2 capture.

Phased Telomere-to-Telomere Reference Genome and Pangenome Reveal an Expansion of Resistance Genes during Apple Domestication.

The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Previous versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the highly heterozygous genome, which impeded genetic studies and breeding programs in apple. In this study, we assembled a haplotype-resolved telomere-to-telomere reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on twelve assemblies from wild and cultivated apples to investigate different types of resistance gene analogs (RGAs). Our results revealed the dynamics of the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Interestingly, our analyses demonstrated a higher prevalence of RGAs in cultivated apples than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Other types of structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR (TNL), NB-ARC-LRR (NL), and CC-NB-ARC-LRR (CNL) genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding programs.

The Impact of Terminal Peptide Extensions of Retinal Inosine 5´Monophosphate Dehydrogenase 1 Isoforms on their DNA-binding Activities.

The main structural difference between the mutation-susceptible retinal isoforms of inosine 5´-monophosphate dehydrogenase-1 (IMPDH-1) with the canonical form resides in the C- and N-terminal peptide extensions with unknown structural/functional impacts. In this report, we aimed to experimentally evaluate the functional impact of these extensions on the specific/non-specific single-stranded DNA (ssDNA)-binding activities relative to those of the canonical form. Our in silico findings indicated the possible contribution of the C-terminal segment to the reduced flexibility of the Bateman domain of the enzyme. In addition, the in silico data indicated that the N-terminal tail acts by altering the distance between the tetramers in the concave octamer complex (the native form) of the enzyme. The overall impact of these predicted structural variations became evident, first, through higher Km values with respect to either of the substrates relative to the canonical isoform, as reported previously (Andashti et al. in Mol Cell Biochem 465(1):155-164, 2020). Secondary, the binding of the recombinant mouse retinal isoform IMPDH1 (603) to its specific Rhodopsin target gene was significantly augmented while its binding to non-specific ssDNA was lower than that of the canonical isoform. The DNA-binding activity of the other mouse retinal isoform, IMPDH1(546), to specific and non-specific ssDNA was lower than that of the canonical form most probably due to the in silico predicted rigidity created in the Bateman domain by the C-terminal peptide extension. Furthermore, the DNA binding to the Rhodopsin target gene by each of the IMPDH isoforms influenced in the presence of GTP (Guanosine triphosphate) and ATP (Adenosine triphosphate).

LcDel: deletion variation detection based on clustering and long reads

Motivation: Genomic structural variation refers to chromosomal level variations such as genome rearrangement or insertion/deletion, which typically involve larger DNA fragments compared to single nucleotide variations. Deletion is a common type of structural variants in the genome, which may lead to mangy diseases, so the detection of deletions can help to gain insights into the pathogenesis of diseases and provide accurate information for disease diagnosis, treatment, and prevention. Many tools exist for deletion variant detection, but they are still inadequate in some aspects, and most of them ignore the presence of chimeric variants in clustering, resulting in less precise clustering results.Results: In this paper, we present LcDel, which can detect deletion variation based on clustering and long reads. LcDel first finds the candidate deletion sites and then performs the first clustering step using two clustering methods (sliding window-based and coverage-based, respectively) based on the length of the deletion. After that, LcDel immediately uses the second clustering by hierarchical clustering to determine the location and length of the deletion. LcDel is benchmarked against some other structural variation detection tools on multiple datasets, and the results show that LcDel has better detection performance for deletion. The source code is available in https://github.com/cyq1314woaini/LcDel.

Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat

Key messagePHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development.The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.

Deciphering male influence in gynogenetic Pengze crucian carp (Carassius auratus var. pengsenensis): insights from Nanopore sequencing of structural variations

In this study, we investigate gynogenetic reproduction in Pengze Crucian Carp (Carassius auratus var. pengsenensis) using third-generation Nanopore sequencing to uncover structural variations (SVs) in offspring. Our objective was to understand the role of male genetic material in gynogenesis by examining the genomes of both parents and their offspring. We discovered a notable number of male-specific structural variations (MSSVs): 1,195 to 1,709 MSSVs in homologous offspring, accounting for approximately 0.52%–0.60% of their detected SVs, and 236 to 350 MSSVs in heterologous offspring, making up about 0.10%–0.13%. These results highlight the significant influence of male genetic material on the genetic composition of offspring, particularly in homologous pairs, challenging the traditional view of asexual reproduction. The gene annotation of MSSVs revealed their presence in critical gene regions, indicating potential functional impacts. Specifically, we found 5 MSSVs in the exonic regions of protein-coding genes in homologous offspring, suggesting possible direct effects on protein structure and function. Validation of an MSSV in the exonic region of the polyunsaturated fatty acid 5-lipoxygenase gene confirmed male genetic material transmission in some offspring. This study underscores the importance of further research on the genetic diversity and gynogenesis mechanisms, providing valuable insights for reproductive biology, aquaculture, and fostering innovation in biological research and aquaculture practices.

Sensitivity Analysis of Modal Parameters of an RC Joint Subject to Progressive Damage under Cyclic Loads

This paper presents the results of an experimental study that focused on the gradual modification of the modal parameters of reinforced concrete beam–column frames subjected to progressive damage under cyclic loading. As is commonly found in structures of the 1970s, the specimen was characterized by the absence of specific shear reinforcement in the nodal panel. The frame modal parameters were investigated using the ambient vibrations test (AVT) as a modal identification technique. In particular, quasi-static cyclic tests with increasing amplitudes were performed on the reinforced concrete frame specimen and the modal parameters were assessed at various stages of frame degradation. By establishing a correlation between the changes in the modal parameters and the mechanical indicators of the structural damage in the frame, this study aimed to determine whether the ambient vibration tests could offer meaningful insights for evaluating the structural health of this type of structural component. As a result of the damage that occurred in the tested RC frame, the residual experimental value of the first natural frequency of the specimen was found to reduce at 52.7% of the original reference value (undamaged stage). Similarly, the residual value of the frame stiffness was found to be as low as 43.82% of the initial one. Both these results confirmed that changes when monitoring the modal frequencies may provide quantitative indexes to describe the structural health of RC frames. In combination with static tests for a direct measure of the structural stiffness variations, the AVT technique was shown to have interesting potential in detecting the type, level, and distribution of the progressive damage in civil structures. In particular, exponential and polynomial regression curves were defined to describe the decay of the first natural frequency as the structural damage increased in various parts of the frame, and it was shown that the variation in the first natural frequency was determined more by the damage on the beam than by the damage on the joint.

Comparative Study on the Duration and Efficacy of Various Botulinum Toxin Type A Injections for Reducing Masseteric Muscle Bite Force and Treating Facial Wrinkles.

Botulinum toxin serotype A (BoNT/A) is widely used for minimal invasive aesthetic treatments. Different brands of BoNT/A exhibit structural variations. The aim of this study was to compare the duration and efficacy of various BoNT/A brands available in Thailand for reducing bite force and treating wrinkles. Fifty participants were randomly assigned to one of five groups, with each group receiving a different BoNT/A brand, namely, incobotulinumtoxinA (IncoA), onabotulinumtoxinA (OnaA), abobotulinumtoxinA (AboA), letibotulinumtoxinA (LetiA), and prabotulinumtoxinA (PraboA). BoNT/A was administered to the masseter muscle and the upper face. Bite force was measured before injection and at 2, 4, 8, 12, 16, 20, and 24weeks post-injection. Evaluation scores for wrinkle improvement were assessed after the treatment. The most significant reduction in bite force occurred between 2 and 4weeks post-injection. PraboA demonstrated the most substantial reduction in bite force, while IncoA had the least effect. However, the percentage of bite force reduction did not exhibit statistical significance between BoNT/A types. Additionally, the reduction in bite force for all BoNT/A types was reversed at 4months post-injection. More than half of the participants experienced improvement beyond 16weeks. The structural differences among BoNT/A brands did not significantly affect the longevity and efficacy of bite force reduction and wrinkle treatment. ClinicalTrials.gov identifier: TCTR20211205001 (registered 4 Dec 2021).

BrBCAT1 mutation resulted in deficiency of epicuticular wax crystal in Chinese cabbage.

BrBCAT1 encoding a branched-chain amino acid aminotransferase was responsible for the glossy trait, which was verified by allelic mutants in Chinese cabbage. The glossy characteristic, thanks to the epicuticular wax crystal deficiency, is an excellent commodity character for leafy vegetables. Herein, two allelic glossy green mutants, wdm11 and wdm12, were isolated from an ethyl methane sulfonate (EMS)-mutagenized population of Chinese cabbage, and the mutant phenotype was recessive inherited. Cryo-SEM detected that epicuticular wax crystal in the mutant leaves was virtually absent. MutMap and Kompetitive allele-specific PCR analyses demonstrated that BraA06g006950.3C (BrBCAT1), homologous to AtBCAT1, encoding a branched-chain amino acid aminotransferase was the candidate gene. A SNP (G to A) on the fourth exon of BrBCAT1 in wdm11 caused the 233rd amino acid to change from glycine (G) to aspartic acid (D). A SNP (G to A) on the second exon of BrBCAT1 in wdm12 led to the 112th amino acid change from glycine (G) to arginine (R). Both of the allelic mutants had genetic structural variation in the candidate gene, which indicated that the mutant phenotype was triggered by the BrBCAT1 mutation. The expression levels of BrBCAT1 and genes related to fatty acid chain extension were decreased significantly in the mutant compared to the wild-type, which might result in epicuticular wax crystal deficiency in the mutants. Our findings proved that the mutation of BrBCAT1 induced the glossy phenotype and provided a valuable gene resource for commodity character improvement in Chinese cabbage.

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.

[Effects of Water Level Fluctuations and Vegetation Restoration on Soil Prokaryotic Microbial Community Structure in the Riparian Zone of the Three Gorges Reservoir].

Riparian zones are typical fragile and sensitive ecological areas. Fluctuations in water level are the main factor affecting the soil environment in these zones, and vegetation restoration is considered an important means of soil conservation there. However, the interactive effects of water level fluctuations and vegetation restoration on the soil microbial community structure in the reservoir riparian zone remain unclear. Therefore, we selected abandoned grassland and artificial forestland at different water level elevations as research objects in the riparian zone of the Three Gorges Reservoir. We used 16S rRNA high-throughput sequencing technology to explore the composition and diversity of soil prokaryotic microbial communities and investigated the main environmental factors driving the soil microbial community structure. The results showed that the α diversity of soil prokaryotes was the highest at the low water level of the riparian zone. The Pielou_e index, Shannon index, and Simpson index at the 163 m elevation were significantly higher than those at the 168 m elevation, and the Chao1 index and Shannon index were significantly higher than those at the 173 m elevation. However, no significant difference was found in the soil microbial community α diversity between abandoned grassland and artificial forestland. At the same time, water level fluctuations and vegetation restoration had significant effects on the community composition of soil prokaryotic microorganisms, and there were significant differences in biomarker categories in different study sites. Notably, the effects of vegetation restoration types on the soil prokaryotic microbial community structure were stronger than that of water level fluctuations. In addition, the results of hierarchical segmentation showed that soil pH was the main driving factor for the change in soil prokaryotic microbial community structure in the Three Gorges Reservoir. These results deepen our understanding of the variations in microbial community structure in the reservoir riparian zone and provide scientific reference for the restoration and reconstruction of the riparian zone ecosystem.

Using multiscale lidar to determine variation in canopy structure from African forest elephant trails

AbstractRecently classified as a unique species by the IUCN, African forest elephants (Loxodonta cyclotis) are critically endangered due to severe poaching. With limited knowledge about their ecological role due to the dense tropical forests they inhabit in central Africa, it is unclear how the Afrotropics are influenced by elephants. Although their role as seed dispersers is well known, they may also drive large‐scale processes that determine forest structure through the creation of elephant trails and browsing the understory, allowing larger, carbon‐dense trees to succeed. Multiple scales of lidar were collected by NASA in Lopé National Park, Gabon from 2015 to 2022. Utilizing two airborne lidar datasets in an African forest elephant stronghold, detailed canopy structural information was used in conjunction with elephant trail data to determine how forest structure varies on and off trails. Forest along elephant trails displayed different structural characteristics than forested areas off trails, with lower canopy height, canopy cover, and different vertical distribution of plant density. Less plant area density was found on trails at 1 m in height, while more vegetation was found at 12 m, compared to off trail locations. Trails in forest areas with previous logging history had lower plant area in the top of the canopy. Forest elephants can be considered as “logging light” ecosystem engineers, affecting canopy structure through browsing and movement. Both airborne lidar scales were able to capture elephant impact along trails, with the high‐resolution discrete return lidar performing higher than waveform lidar.

Evaluation of influence of wall roughness on wall turbulence using LES simulation with MSGD model for liquid Li flow inside two-staged contraction nozzle

ABSTRACT Liquid lithium (Li) jet is planned as a beam target in fusion neutron sources (FNSs), such as IFMIF, A-FNS and IFMIF-DONES. For the safety and the efficiency of such FNSs, the high-speed Li jet need to be kept stable. For investigation of the detailed flow pattern inside the Li jet, numerical approaches using CFD simulation have been required to evaluate it because of its opacity. As one of issues about the inner flow structure, the influence of wall roughness on the vortex structure and surface variation is concerned in long-term operation of actual FNSs. In our previous simulation, in order to consider wall roughness in LES simulation, MSGD model was adopted to ANSYS Fluent using User-Defined Function, and CFD simulation in a simple parallel plate flow was conducted to confirm the performance of MSGD model. In this study, firstly, MSGD model was verified by LES simulation of Li flowing on smooth and rough plates. After that, LES simulation with MSGD model for two-staged contraction nozzle, installed into Li loop of Osaka University, was conducted. It was found that MSGD model was valid and spectrum of velocity in roughness wall cases clearly had different behavior from that in smooth wall case.

The genomic landscape of Vk*MYC myeloma highlights shared pathways of transformation between mice and humans

Multiple myeloma (MM) is a heterogeneous disease characterized by frequent MYC translocations. Sporadic MYC activation in the germinal center of genetically engineered Vk*MYC mice is sufficient to induce plasma cell tumors in which a variety of secondary mutations are spontaneously acquired and selected over time. Analysis of 119 Vk*MYC myeloma reveals recurrent copy number alterations, structural variations, chromothripsis, driver mutations, apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC) mutational activity, and a progressive decrease in immunoglobulin transcription that inversely correlates with proliferation. Moreover, we identify frequent insertional mutagenesis by endogenous retro-elements as a murine specific mechanism to activate NF-kB and IL6 signaling pathways shared with human MM. Despite the increased genomic complexity associated with progression, advanced tumors remain dependent on MYC. In summary, here we credential the Vk*MYC mouse as a unique resource to explore MM genomic evolution and describe a fully annotated collection of diverse and immortalized murine MM tumors.