Search

The elemental dynamics and interactions within deadwood profoundly influence carbon sequestration and nutrient cycling in forest ecosystems. Recent studies have investigated macronutrient cycling during deadwood decay of specific plants, yet the dynamics and interactions of micronutrients, trace elements, and the elementome across species and decay stages remain unexplored. Here, we investigated the elementome and their coupling relationships across five decay stages of downed deadwood (DDW) from four dominant species (Hippophae rhamnoides, Populus purdomii, Abies fabri, and Picea brachytyla) along the Hailuogou Glacier primary successional chronosequence. Element coupling was evaluated following the framework of mean correlation of all elements in absolute value and null modeling. We observed species-specific elementome differentiation during DDW decay, with interspecific distances greater in the initial and later decay stages and lower in the intermediate stage. Notably, shrub H. rhamnoides exhibited distinct initial elementomes and remained robust multi-element coupling throughout decay. Conversely, element couplings for tree species declined with decay, particularly for P. purdomii and A. fabri, reaching decoupling from Stage III. Non-essential elements of Al, V, and Ti remained robust coupling, while key nutrients of N, P, and Ca decoupled as decay progressed. The individual element coupling was negatively correlated with their enrichment levels, with lower coupling observed for anthropogenically enriched metals. Our results reveal the importance of plant species in elementome differentiation and element coupling during deadwood decay, while atmospheric heavy metal deposition mediates individual element coupling, underscoring species-specific deadwood management strategies and monitoring of heavy metal deposition to optimize forest ecosystem functions and stability., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Plant genebanks contain large numbers of germplasm accessions that likely harbor useful alleles or genes absent in commercial plant breeding programs. Broadening the genetic base of commercial alfalfa germplasm with these valuable genetic variations can be achieved by screening the extensive genetic diversity in germplasm collections and enabling maximal recombination among selected genotypes. In this study, we assessed the genetic diversity and differentiation of germplasm pools selected in northern U.S. latitudes (USDA Plant Hardiness Zone 7 or below) originating from Eurasian germplasm. The germplasm evaluated included four BASE populations (C0) from different geographical origins (Central Asia, Northeastern Europe, Balkans-Turkey-Black Sea, and Siberia/Mongolia), 20 cycle-one populations (C1) derived from each of the four BASE populations selected across five locations in the U.S. and Canada, and four commercial cultivars. Using a panel of 3,000 Diversity Array Technologies (DArTag) marker loci, we retrieved 2,994 target SNPs and approximately 12,000 microhaplotypes. Microhaplotypes exhibited higher genetic diversity values than target SNPs. Principal component analysis and discriminant analysis of principal components revealed significant population structure among the alfalfa populations based on geographical origin, while the check cultivars formed a central cluster. Inbreeding coefficients (F IS ) ranged from - 0.1 to 0.006, with 27 out of 28 populations showing negative F IS values, indicating an excess of heterozygotes. Interpopulation genetic distances were calculated using Rho pairwise distances (F ST adapted for autotetraploid species) and analysis of molecular variance (AMOVA) parameters. All BASE populations showed lower Rho values compared to C1 populations and check cultivars. AMOVA revealed that most of the genetic diversity was among individuals within populations, especially in BASE populations (92.7%). This study demonstrates that individual plants in BASE populations possess high genetic diversity, low interpopulation distances, and minimal inbreeding, characteristics that are essential for base-broadening selection. The populations developed in this project serve as valuable sources of novel alleles for North American alfalfa breeding programs, offering breeders access to diverse, regionally adapted pools for improving various alfalfa traits., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2025. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Vegetation restoration in metallic tailing reservoirs is imperative to restore the post-mining degraded ecosystems. Extracellular enzymes determine microbial resource acquisition in soils, yet the mechanisms controlling the enzyme activity and stoichiometry during vegetation restoration in metallic tailing reservoirs remain elusive. Here, we investigated the variations and drivers of C-, N- and P-acquiring enzymes together with microbial community along a 50-year vegetation restoration chronosequence in the China's largest vanadium titano-magnetite tailing reservoir. We found a parabolic pattern in the enzyme activity and efficiency along the chronosequence, peaking at the middle restoration stage (∼30 years) with approximately six-fold increase relative to the initial 1-year site. The enzyme ratios of C:P and N:P decreased by 33 % and 68 % along the chronosequence, respectively, indicating a higher microbial demand of C and N at the early stage and a higher demand of P at the later stage. Soil nutrients directly determined the enzyme activities and stoichiometry, whereas microbial biomass and community structure regulated the temporal pattern of the enzyme efficiency. Surprisingly, increased heavy metal pollution imposed a positive effect on the enzyme efficiency indirectly by altering microbial community structure. This was evidenced by the increased microbial diversity and the conversion of copiotrophic to oligotrophic and stress-tolerant taxa along the chronosequence. Our findings provide new insights into microbial functioning in soil nutrient dynamics during vegetation restoration under increasing heavy metal pollution., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Microorganisms are pivotal in sustaining soil functions, yet the specific contributions of bacterial and fungal succession on the functions during vegetation restoration in metallic tailing reservoirs remains elusive. Here, we explored bacterial and fungal succession and their impacts on soil multifunctionality along a ∼50-year vegetation restoration chronosequence in China's largest vanadium titano-magnetite tailing reservoir. We found a significant increase in soil multifunctionality, an index comprising factors pertinent to soil fertility and microbially mediated nutrient cycling, along the chronosequence. Despite increasing heavy metal levels, both bacterial and fungal communities exhibited significant increase in richness and network complexity over time. However, fungi demonstrated a slower succession rate and more consistent composition than bacteria, indicating their relatively higher resilience to environmental changes. Soil multifunctionality was intimately linked to bacterial and fungal richness or complexity. Nevertheless, when scrutinizing both richness and complexity concurrently, the correlations disappeared for bacteria but remained robust for fungi. This persistence reveals the critical role of the fungal community resilience in sustaining soil multifunctionality, particularly through their stable interactions with powerful core taxa. Our findings highlight the importance of fungal succession in enhancing soil multifunctionality during vegetation restoration in metallic tailing reservoirs, and manipulating fungal community may expedite ecological recovery of areas polluted with heavy metals., Competing Interests: Declaration of Competing Interest The authors declare that they do not have any competing interests that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Accurate measurement of a Radar Cross-Section (RCS) is a critical technical challenge in assessing the stealth performance and scattering characteristics of radar targets. Traditional RCS measurement methods are limited by high costs, sensitivity to environmental conditions, and difficulties in distinguishing local scattering features of targets. To address these challenges, this paper proposes a novel RCS measurement method based on enhanced imaging and scattering center extraction. This method integrates sub-aperture imaging with image fusion techniques to improve imaging quality and enhance the detail of target scattering characteristics. Additionally, an improved sequence CLEAN algorithm is employed to effectively suppress sidelobe effects and ensure the accuracy of scattering center extraction. Experimental results demonstrate that this method achieves higher precision in RCS measurement of complex targets and is particularly effective in environments with strong interference, where it successfully separates the scattering contributions of the target from those of the interference sources. This method offers a new technological approach for precise RCS measurement of radar stealth targets in the future.

Objective: Bipolar disorder (BD) is a debilitating neuropsychiatric disorder, which is associated with genetic variation through "vast but mixed" Genome-Wide Association Studies (GWAS). Transcriptome-Wide Association Study (TWAS) is more effective in explaining genetic factors that influence complex diseases and can help identifying risk genes more reliably. So, this study aims to identify potential BD risk genes in pedigrees with TWAS., Methods: We conducted a TWAS analysis with expression quantitative trait loci (eQTL) analysis on extended BD pedigrees, and the BD genome-wide association study (GWAS) summary data acquired from the Psychiatric Genomics Consortium (PGC). Furthermore, the BD-associated genes identified by TWAS were validated by mRNA expression profiles from the Gene Expression Omnibus (GEO) Datasets (GSE23848 and GSE46416). Functional enrichment and annotation analysis were implemented by RStudio (version 4.2.0)., Results: TWAS identified 362 genes with P value < 0.05, and 18 genes remain significant after Bonferroni correction, such as SEMA3G (P TWAS =1.07 × 10 -11 ), ALOX5AP (P TWAS =3.12 × 10 -8 ), and PLEC (P TWAS =1.27 × 10 -7 ). Further 6 overlapped genes were detected in integrative analysis, such as UQCRB (P TWAS =0.0020, P mRNA =0.0000), TMPRSS9 (P TWAS =0.0405, P mRNA =0.0032), and SNX10 (P TWAS =0.0104, P mRNA =0.0015). Using genes identified by TWAS, Gene Ontology (GO) enrichment analysis identified 40 significant GO terms, such as mitochondrial ATP synthesis coupled electron transport, mitochondrial respiratory, aerobic electron transport chain, oxidative phosphorylation, mitochondrial membrane proteins, and ubiquinone activity. The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway enrichment analysis identified significant 15 pathways for BD, such as Oxidative phosphorylation, endocannabinoids signaling, neurodegeneration, and reactive oxide species., Conclusions: We found a set of BD-associated genes and pathways, validating the important role of neurodevelopmental abnormalities, inflammatory responses, and mitochondrial dysfunction in the pathology of BD, offering novel information for comprehending the genetic basis of BD., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Alfalfa biomass can be fractionated into leaf and stem components. Leaves comprise a protein-rich and highly digestible portion of biomass for ruminant animals, while stems constitute a high fiber and less digestible fraction, representing 50 to 70% of the biomass. However, little attention has focused on stem-related traits, which are a key aspect in improving the nutritional value and intake potential of alfalfa. This study aimed to identify molecular markers associated with four morphological traits in a panel of five populations of alfalfa generated over two cycles of divergent selection based on 16-h and 96-h in vitro neutral detergent fiber digestibility in stems. Phenotypic traits of stem color, presence of stem pith cells, winter standability, and winter injury were modeled using univariate and multivariate spatial mixed linear models (MLM), and the predicted values were used as response variables in genome-wide association studies (GWAS). The alfalfa panel was genotyped using a 3K DArTag SNP markers for the evaluation of the genetic structure and GWAS. Principal component and population structure analyses revealed differentiations between populations selected for high- and low-digestibility. Thirteen molecular markers were significantly associated with stem traits using either univariate or multivariate MLM. Additionally, support vector machine (SVM) and random forest (RF) algorithms were implemented to determine marker importance scores for stem traits and validate the GWAS results. The top-ranked markers from SVM and RF aligned with GWAS findings for solid stem pith, winter standability, and winter injury. Additionally, SVM identified additional markers with high variable importance for solid stem pith and winter injury. Most molecular markers were located in coding regions. These markers can facilitate marker-assisted selection to expedite breeding programs to increase winter hardiness or stem palatability., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Medina, Heuschele, Zhao, Lin, Beil, Sheehan and Xu.)

Salvia hispanica L. (Chia), a member of the Lamiaceae, is an economically important crop in Mesoamerica, with health benefits associated with its seed fatty acid composition. Chia varieties are distinguished based on seed color including mixed white and black (Chia pinta) and black (Chia negra). To facilitate research on Chia and expand on comparative analyses within the Lamiaceae, we generated a chromosome-scale assembly of a Chia pinta accession and performed comparative genome analyses with a previously published Chia negra genome assembly. The Chia pinta and Chia negra genome sequences were highly similar as shown by a limited number of single nucleotide polymorphisms and extensive shared orthologous gene membership. However, there is an enrichment of terpene synthases in the Chia pinta genome relative to the Chia negra genome. We sequenced and analyzed the genomes of 20 Chia accessions with differing seed color and geographic origin revealing population structure within S. hispanica and interspecific introgressions of Salvia species. As the genus Salvia is polyphyletic, its evolutionary history remains unclear. Using large-scale synteny analysis within the Lamiaceae and orthologous group membership, we resolved the phylogeny of Salvia species. This study and its collective resources further our understanding of genomic diversity in this food crop and the extent of interspecies hybridizations in Salvia., (© 2024 The Author(s). The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.)

Background: To analyze the clinical characteristics of ureteropelvic junction obstruction (UPJO) caused by crossing vessels (CV) in infants and young children., Methods: A retrospective analysis was performed on children with UPJO who underwent primary surgery. Patients were classified into laparoscopic pyeloplasty (LP) and open pyeloplasty (OP) groups and classified as ≤3 or >3 (years old) groups. Children with CV-caused UPJO were identified., Results: A total of 747 patients were included. Ninety cases of CV were identified. The CV discovery rate was higher in the LP group (78/457, 17.1%) than in the OP group (12/290, 4.1%) (P < 0.001). In the ≤3 group, the CV discovery rate in the LP group (27/144, 18.8%) was higher than that in the OP group (11/274, 4.0%) (P < 0.001). In the LP group, there was no significant difference between ≤3 (27/144, 18.8%) and >3 (51/313, 16.3%) groups in the CV discovery rate. The rate in children with UPJO was not significantly different at any age (P > 0.05). Progressive aggravation of hydronephrosis (21/27, 77.8%) and symptomatic hydronephrosis (44/51, 86.3%) were the main surgical indications in the ≤3 and > 3 groups, respectively. There were no preoperatively confirmed cases of CV in the ≤3 group. In the OP group, five patients underwent reoperation, three of whom were due to failure to detect CV during the initial operation., Conclusions: The CV distribution is similar in children with UPJO across all ages; CV in infants and young children are not rare. LP should be considered as CV are prone to being missed during OP., Levels of Evidence: III., Competing Interests: Conflicts of interest The authors declare that there is no conflict of interest., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Small public breeding programs focused on specialty crops have many barriers to adopting technology, particularly creating and using genetic marker panels for genomic-based decisions in selection. Here, we report the creation of a DArTag panel of 3120 loci distributed across the sweetpotato ( Ipomoea batatas [L.] Lam) genome for molecular-marker-assisted breeding and genomic prediction. The creation of this marker panel has the potential to bring cost-effective and rapid genotyping capabilities to sweetpotato breeding programs worldwide. The open access provided by this platform will allow the genetic datasets generated on the marker panel to be compared and joined across projects, institutions, and countries. This genotyping resource has the power to make routine genotyping a reality for any breeder of sweetpotato.

Annual medic ( Medicago spp.) germplasm was collected from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the United States department of Agriculture, Agricultural Research Service, National Plant Germplasm System (NPGS) temperate-adapted forage legume collection. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. Phenotyping included the use of 24 descriptor traits while genetic characterization was accomplished using a 3K Diversity Array Technologies (DArTag) panel developed for alfalfa ( Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was limited, resulting in an average of ~1,500 marker loci detected per species. From these loci, 448 markers were present in 95% of the samples. Principal component and phylogenetic analysis based on a larger set of 2,396 selected markers clustered accessions by species and predicted evolutionary relationships among species. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between single (n=3) and pooled (n=7) biological replicate leaf samples. The phenotyping and the 2,396 Single Nucleotide Polymorphism (SNP) marker set were useful in estimating population structure in the Crimean and reference accessions, highlighting novel and unique genetic diversity captured in the Crimean accessions. This research not only demonstrated the utility of the DArTag marker panel in evaluating the Crimean germplasm but also highlighted its broader application in assessing genetic resources within the Medicago genus. Furthermore, we anticipate that our findings will underscore the importance of leveraging genetic resources and advanced genotyping tools for sustainable crop improvement and biodiversity conservation in annual medic species., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Zhao, Sapkota, Lin, Beil, Sheehan, Greene and Irish.)

Background: Lower extremity motor dysfunction is one of the most severe consequences after stroke, restricting functional mobility and impairing daily activities. Growing evidence suggests that repetitive transcranial magnetic stimulation (rTMS) can improve stroke patients' lower extremity motor function. However, there is still controversy about the optimal rTMS protocol. Therefore, we compared and analyzed the effects of different rTMS protocols on lower extremity motor function in stroke patients using network meta-analysis (NMA)., Methods: We systematically searched CNKI, WanFang, VIP, CBM, PubMed, Embase, Web of Science, and Cochrane Library databases (from origin to 31 December 2023). Randomized controlled trials (RCTs) or crossover RCTs on rTMS improving lower extremity motor function in stroke patients were included. Two authors independently completed article screening, data extraction, and quality assessment. RevMan (version 5.4) and Stata (version 17.0) were used to analyze the data., Results: A total of 38 studies with 2,022 patients were eligible for the NMA. The interventions included HFrTMS-M1, LFrTMS-M1, iTBS-Cerebellum, iTBS-M1, dTMS-M1, and Placebo. The results of NMA showed that LFrTMS-M1 ranked first in FMA-LE and speed, and HFrTMS-M1 ranked first in BBS, TUGT, and MEP amplitude. The subgroup analysis of FMA-LE showed that HFrTMS-M1 was the best stimulation protocol for post-stroke time > 1 month, and LFrTMS-M1 was the best stimulation protocol for post-stroke time ≤ 1 month., Conclusion: Considering the impact of the stroke phase on the lower extremity motor function, the current research evidence shows that HFrTMS-M1 may be the preferred stimulation protocol to improve the lower extremity motor function of patients for post-stroke time > 1 month, and LFrTMS-M1 for post-stroke time ≤ 1 month. However, the above conclusion needs further analysis and validation by more high-quality RCTs. Systematic Review Registration: www.crd.york.ac.uk/prospero/, identifier (CRD42023474215)., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Wang, Zhang, Zhang, Zhao, Xu, Liu, Wu, Wu, Yong and Wu.)

Vitamin B12 plays a role in DNA methylation, influencing the 1-carbon cycle; However, its effect on colorectal cancer (CRC) mortality remains uncertain. This study assessed the relationship between vitamin B12 intake and all-cause and cancer-specific mortality among CRC patients. We analyzed data from the NHANES from 1999 to 2018, using multivariable Cox regression, competing risk model, Kaplan-Meier survival curves, and stratified analysis with interaction effects. The studied involved 4,554 cancer patients (mean age 65.8 years, 47.6% males). Results from multivariate Cox regression indicated that each additional 1 mcg/day of dietary vitamin B12 independently increased the risk of all-cause (HR, 1.07; 95% CI: 1.04-1.09, p  < 0.001) and cancer-specific mortality (HR, 1.04; 95% CI, 1.02-1.06; p  < 0.001). Kaplan-Meier curves indicated a higher risk of all-cause mortality with increased vitamin B12 intake (Log rank p  = 0.01). Subgroup analysis suggested that higher vitamin B12 intake correlated with increased all-cause mortality risk, especially in individuals with higher protein (HR, 1.04; 95% CI, 1.02-1.06; p  = 0.019) or carbohydrate intake (HR, 1.03; 95% CI, 1.01-1.05; p  = 0.04). Thus, higher vitamin B12 intake correlates with increased all-cause and cancer-specific mortality in CRC patients, particularly those with higher protein or carbohydrate intake.

The development of mobile networks has led to the emergence of challenges such as high delays in storage, computing and traffic management. To deal with these challenges, fifth-generation networks emphasize the use of technologies such as mobile cloud computing and mobile edge computing. Mobile Edge Cloud Computing (MECC) is an emerging distributed computing model that provides access to cloud computing services at the edge of the network and near mobile users. With offloading tasks at the edge of the network instead of transferring them to a remote cloud, MECC can realize flexibility and real-time processing. During computation offloading, the requirements of Internet of Things (IoT) applications may change at different stages, which is ignored in existing works. With this motivation, we propose a task offloading method under dynamic resource requirements during the use of IoT applications, which focuses on the problem of workload fluctuations. The proposed method uses a learning automata-based offload decision-maker to offload requests to the edge layer. An auto-scaling strategy is then developed using a long short-term memory network which can estimate the expected number of future requests. Finally, an Asynchronous Advantage Actor-Critic algorithm as a deep reinforcement learning-based approach decides to scale down or scale up. The effectiveness of the proposed method has been confirmed through extensive experiments using the iFogSim simulator. The numerical results show that the proposed method has better scalability and performance in terms of delay and energy consumption than the existing state-of-the-art methods., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2023 The Author(s).)

Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing and aquaculture industries. Large differences exist between the genomes of Atlantic salmon of European origin and North American (N.A.) origin. Given the genetic and genomic differences between the 2 lineages, it is crucial to develop unique genomic resources for N.A. Atlantic salmon. Here, we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon aquaculture. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole-genome resequencing of 80 N.A. Atlantic salmon individuals. Secondly, a high-density 50K SNP array enriched for the genic regions of the genome and containing 3 sex determination and 61 putative continent of origin markers was developed and validated. Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers was generated from 2,512 individuals in 141 full-sib families. Finally, a chromosome-level de novo genome assembly from a male N.A. Atlantic salmon from the St. John River aquaculture strain was generated using PacBio long reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of the conserved Actinopterygii genes in the assembly, and the genetic linkage information was used to guide the formation of 27 chromosome sequences. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the 2 lineages are caused by a fission in chromosome Ssa01 and 3 chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29, and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species., Competing Interests: Conflicts of interest statement The authors declare no conflict of interest., (Published by Oxford University Press on behalf of The Genetics Society of America 2023.)

The sweetpotato weevil, Cylas formicarius elegantulus (Summers) (Coleoptera: Brentidae), is one of the most destructive pests of sweetpotato worldwide. Genomic analyses of sweetpotato weevils can provide insights into their genetic diversity, population structure, and dispersal as well as provide information to support management strategies. Adult sweetpotato weevils were collected by various methods from Ipomoea batatas L. (sweetpotato) or I. coccinea L. (red morning glory) in the U.S. states of Georgia, Hawaii, South Carolina, and Texas. Genomic DNA was extracted from individual weevil specimens and sequenced using Illumina NovaSeq. A total of 181 GB of 150 base pair (bp) paired-end reads were generated for 40 specimens. Mitochondrial genomes were assembled for each specimen via reference mapping and annotated using Geneious Prime. Full mitochondrial genome sequences range from 17,141 to 17,152 bp with an average GC content of 21.8% and average coverage of 3307 × . A maximum likelihood phylogenetic analysis considering the mitochondrial protein coding genes is provided. Mitochondrial genomes and assembled reads are deposited in NCBI GenBank, providing 40 mitogenomes of C. formicarius elegantulus collected in the U.S.

Colorectal cancer (CRC) is an extremely lethal disease worldwide. However, the underlying pathogenesis remains unclear. This study aimed to reveal the distinct characteristics of age-stratified CRC at the protein level and explore precise treatment targets. Patients who underwent surgical removal with pathologically confirmed CRC at China-Japan Friendship Hospital from January 2020 to October 2021 were recruited, cancer and para-carcinoma tissues (> 5 cm) were detected by mass spectrometry. Ninety-six clinical samples were collected and divided into three groups according to age: young (≤ 50 years), middle-aged (51-69 years), and old (≥ 70 years). Quantitative proteomic analysis was performed, as well as comprehensive bioinformatic analysis based on the Human Protein Atlas, Clinical Proteomic Tumor Analysis Consortium and Connectivity Map databases. The numbers of upregulated and downregulated proteins were 1315 and 560 in the young group, 757 and 311 in the old group, and 1052 and 468 in the middle-aged group, respectively. Bioinformatic analysis showed that these differentially expressed proteins had different molecular functions and participated in extensive signaling pathways. We also revealed ADH1B, ARRDC1, GATM, GTF2H4, MGME1, and LILRB2 as possible cancer-promoting molecules, which might serve as potential prognostic biomarkers and precise therapeutic targets for CRC. SIGNIFICANCE: This study comprehensively characterized the proteomic profiles of age-stratified colorectal cancer patients, focusing on the differentially expressed proteins between cancer and paracancerous tissues in different age groups, in an effort to find corresponding potential prognostic biomarkers and therapeutic targets. In addition, this study provides potentially valuable clinical small molecule inhibitory agents., Competing Interests: Declaration of Competing Interest On behalf of all authors, the corresponding author states that there is no conflict of interest., (Copyright © 2023 Elsevier B.V. All rights reserved.)

The emerging market of wearable devices for tracking and positioning requires the development of highly flexible magnetic sensors. Due to the stable magnetoresistance ratio and simple fabrication process, sensors based on the anisotropic magnetoresistance (AMR) effect have been proposed as promising candidates. However, the stability of AMR sensors under different bending situations has rarely been investigated. In this work, we proposed a flexible AMR magnetic sensor deposited on an ultra-thin Kapton substrate, which exhibits excellent anti-fatigue behavior at different bending curvatures ranging from 1/3 to 1/10 mm-1. Experimental results show that the sensitivity of our proposed flexible AMR sensor remains as high as 0.25 Oe-1 after being bent 500 times, showing promising potential for application in wearable electronic devices., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)

Objective: To compare the characteristics of conventional laparoscopic pyeloplasty (LP) and robotic-assisted laparoscopic pyeloplasty (RALP) in infants and young children with ureteropelvic junction obstruction (UPJO)., Methods: We performed a retrospective study of patients (age: 0-36 months) who underwent dismembered pyeloplasty (Anderson-Hynes) with the fourth-generation RALP or traditional LP between April 2020 and December 2020., Results: A total of 33 patients with UPJO were enrolled: 12 underwent RALP (9 left side; 3 right side) and 21 underwent LP (18 left side; 3 right side). In the RALP group, the median patient age was 17 months (range: 5-36 months). In the LP group, the median patient age was 9 months (range: 2-36 months) (P = 0.182). The mean operation times were 120.25 ± 37.54 min (RALP) and 156.10 ± 51.11 min (LP) (P = 0.042), and the mean lengths of hospital stay were 6.42 ± 1.62 days (RALP) and 8.19 ± 2.25 days (LP) (P = 0.023). Removal of the drainage tube was performed after 3.08 ± 0.69 days (RALP) and after 4.76 ± 1.81 days (LP) (P = 0.001). The postoperative pain showed no significant difference. The mean hospitalization costs were 61464.75 ± 2800.53 yuan (RALP) and 22169.52 ± 3442.15 yuan (LP) (P < 0.001). The mean follow-up time was 10-18 months. Significant improvements in the anteroposterior diameter and parenchymal thickness were observed after surgery. Conversion to laparotomy was not performed. No short-term complications occurred during postoperative hospitalization and follow-up., Conclusion: RALP has the advantages of less trauma and faster recovery. It can be safely and effectively performed in infants and young children, and its effectiveness is similar to that of traditional LP., Competing Interests: Declaration of competing interest The Authors declare that there is no conflict of interest., (Copyright © 2023 Asian Surgical Association and Taiwan Robotic Surgery Association. Published by Elsevier B.V. All rights reserved.)

Cornelia de Lange syndrome (CdLS) is a rare genetic disease involving multiorgan systems that varies in clinical manifestations. Female genital abnormalities in patients with CdLS are rarely reported, and current guidelines for CdLS contain little information related to female genital abnormalities. We report a case of classic CdLS with an NIPBL gene pathogenic variant in a 4.5-year-old girl who experienced recurrent urinary tract infections (UTIs) with vesical tenesmus. Urogenital physical and imaging examinations revealed external vaginal orifice obstruction and bilateral vesicoureteral reflux (VUR). Vaginal diaphragm-like tissue resection and vaginal orifice plasty were performed on this patient. The symptoms of urination disorders and recurrent UTIs, as well as VUR grading, improved after relieving the vaginal obstruction during the operation. For female CdLS patients, especially those with VUR, it is necessary to check for genital abnormalities and perform timely treatment, which is of great significance in improving urination disorder symptoms, reducing resistance during voiding, decreasing the occurrence of secondary VUR, and controlling recurrent UTIs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Shen, Zhao, Sun, Yang and Yan.)

Thousands of natural products are derived from the fused cyclopentane-pyran molecular scaffold nepetalactol. These natural products are used in an enormous range of applications that span the agricultural and medical industries. For example, nepetalactone, the oxidized derivative of nepetalactol, is known for its cat attractant properties as well as potential as an insect repellent. Most of these naturally occurring nepetalactol-derived compounds arise from only two out of the eight possible stereoisomers, 7S-cis-trans and 7R-cis-cis nepetalactols. Here we use a combination of naturally occurring and engineered enzymes to produce seven of the eight possible nepetalactol or nepetalactone stereoisomers. These enzymes open the possibilities for biocatalytic production of a broader range of iridoids, providing a versatile system for the diversification of this important natural product scaffold., (© 2022. The Author(s).)

Background: To investigate the effects of taurine on prostate cancer cell proliferation and apoptosis, and on the mammalian sterilization of a 20-like kinase-1 ( MST1 )/ Hippo signaling pathway., Methods: The prostate cancer DU145 cell line was selected and the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method was used to determine the rate of inhibition by taurine on the proliferation of the cells at 1, 10 -1 , 10 -2 , 10 -3 , 10 -4 , 10 -5 and 10 -6 mg/mL to obtain the taurine intervention concentrations. The cultured cells were divided into three groups: the blank group was cultured with conventional culture medium, the positive control group was cultured with 2 mg/mL cisplatin, and the taurine group was cultured with the determined taurine intervention concentrations of 0.003 mg/mL as low, 0.03 mg/mL as medium and 0.3 mg/mL as high concentration. After 72 h incubation, cell proliferation, apoptosis and cellular MST1 / Hippo signaling pathway protein expression were observed., Results: In the comparison of cell proliferation rate, the taurine group was lower than the positive control group and the blank group (P<0.05), the cell proliferation rate of different concentrations in the taurine group decreased with the increase of concentration (P<0.05). The apoptosis rate was higher in the taurine group than in the positive control group and the blank group (P<0.05), the apoptosis rate increased with increasing concentration in the taurine group (P<0.05). The expression of MST1 and Bax was higher in the taurine group than in the positive control group and the blank group (P<0.05), the expression of MST1 and Bax increased with increasing concentration in the taurine group (P<0.05). The expression of YAP and Bcl-2 was lower in the taurine group than in the positive control group and the blank group (P<0.05), the expression of YAP and Bcl-2 decreased with increasing concentration in the taurine group (P<0.05)., Conclusions: Taurine promoted apoptosis and inhibited proliferation of prostate cancer cells, and its mechanism of action may be related to the MST1 / Hippo signaling pathway in a dose-dependent manner., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tcr.amegroups.com/article/view/10.21037/tcr-22-1297/coif). The authors have no conflicts of interest to declare., (2022 Translational Cancer Research. All rights reserved.)

In recent years, compute-in-memory (CIM) has been extensively studied to improve the energy efficiency of computing by reducing data movement. At present, CIM is frequently used in data-intensive computing. Data-intensive computing applications, such as all kinds of neural networks (NNs) in machine learning (ML), are regarded as 'soft' computing tasks. The 'soft' computing tasks are computations that can tolerate low computing precision with little accuracy degradation. However, 'hard' tasks aimed at numerical computations require high-precision computing and are also accompanied by energy efficiency problems. Numerical computations exist in lots of applications, including partial differential equations (PDEs) and large-scale matrix multiplication. Therefore, it is necessary to study CIM for numerical computations. This article reviews the recent developments of CIM for numerical computations. The different kinds of numerical methods solving partial differential equations and the transformation of matrixes are deduced in detail. This paper also discusses the iterative computation of a large-scale matrix, which tremendously affects the efficiency of numerical computations. The working procedure of the ReRAM-based partial differential equation solver is emphatically introduced. Moreover, other PDEs solvers, and other research about CIM for numerical computations, are also summarized. Finally, prospects and the future of CIM for numerical computations with high accuracy are discussed.

The plasmon resonances of grating-gated AlN/GaN HEMTs can occur in wide frequency regions at mid-infrared frequencies. However, the lack of polarization properties research in grating-gated AlN/GaN HEMTs prevents the application potential. In order to solve the problem, the polarization properties in grating-gated AlN/GaN HEMTs at mid-infrared frequencies were studied in the paper. After using the optical transfer matrix method to calculate the dispersion curves in grating-gated AlN/GaN HEMTs, the plasmon polaritons in conductive channel and phonon polaritons in GaN layer occur under TM incident waves rather than TE incident waves. The phenomenon illustrates the potential of polarization-selectivity has existed in grating-gated AlN/GaN HEMTs. To study the polarization properties of grating-gated AlN/GaN HEMTs in detail, the electric field distribution and transmission properties of the structure were simulated in COMSOL. The results show the excellent polarization-selectivity at mid-infrared frequencies in grating-gated AlN/GaN HEMTs. The studies of these characteristics indicate the vast potential for using grating-gated AlN/GaN HEMTs to design mid-infrared polarizers, mid-infrared polarization state modulators and other devices in the future.

A novel VDMOS with Step Floating Islands VDMOS (S-FLI VDMOS) is proposed for the first time in this letter, in order to optimize the breakdown voltage ( BV ) and the specific on-resistance ( R on,sp ). The innovative terminal technology of Breakdown Point Transfer (BPT) is applied to S-FLI VDMOS, which transfers the breakdown point from the high electric field region to the low electric field region, and the S-FLI VDMOS structure uses multiple layers of charge compensation blocks to generate multiple electric field peaks in the drift region in order to optimize the electric field distribution. In the TCAD simulation, the BV of the proposed S-FLI VDMOS is improved to 326 V, which is higher than that of 281 V for the conventional Si VDMOS with the same drift region length of 15 μm, and the R on,sp is reduced from 21.54 mΩ·cm 2 for the conventional Si VDMOS to 7.77 mΩ·cm 2 for the S-FLI VDMOS. Compared with the conventional Si VDMOS, the current density of the effective current conduction path is increased when the forward bias is applied to the proposed device.

A variety of mutations in the androgen receptor (AR) gene are linked to androgen insensitivity syndrome (AIS). AIS is the most common specific cause of 46, XY disorder in sex development. Here, we reported a patient which presented as a female with 46, XY karyotype and normal female external genitalia. The patient was diagnosed with complete AIS caused by a novel mutation (NM&#95;000044, c.2678-2726del, p. Pro893Leufs*35) in the AR gene. Targeted exome sequencing was used to detect the patient's androgen receptor gene mutations. Sanger sequencing was used to validate the mutation. This study showed that a novel mutation of the AR gene can cause complete AIS; the study also broadened the AR mutation spectrum and indicated that targeted exome sequencing could help facilitate the diagnosis of complicated disorders in sexual development., (© 2021 Wiley-VCH GmbH.)

Thymol and carvacrol are phenolic monoterpenes found in thyme, oregano, and several other species of the Lamiaceae. Long valued for their smell and taste, these substances also have antibacterial and anti-spasmolytic properties. They are also suggested to be precursors of thymohydroquinone and thymoquinone, monoterpenes with anti-inflammatory, antioxidant, and antitumor activities. Thymol and carvacrol biosynthesis has been proposed to proceed by the cyclization of geranyl diphosphate to γ-terpinene, followed by a series of oxidations via p -cymene. Here, we show that γ-terpinene is oxidized by cytochrome P450 monooxygenases (P450s) of the CYP71D subfamily to produce unstable cyclohexadienol intermediates, which are then dehydrogenated by a short-chain dehydrogenase/reductase (SDR) to the corresponding ketones. The subsequent formation of the aromatic compounds occurs via keto-enol tautomerisms. Combining these enzymes with γ-terpinene in in vitro assays or in vivo in Nicotiana benthamiana yielded thymol and carvacrol as products. In the absence of the SDRs, only p -cymene was formed by rearrangement of the cyclohexadienol intermediates. The nature of these unstable intermediates was inferred from reactions with the γ-terpinene isomer limonene and by analogy to reactions catalyzed by related enzymes. We also identified and characterized two P450s of the CYP76S and CYP736A subfamilies that catalyze the hydroxylation of thymol and carvacrol to thymohydroquinone when heterologously expressed in yeast and N. benthamiana Our findings alter previous views of thymol and carvacrol formation, identify the enzymes involved in the biosynthesis of these phenolic monoterpenes and thymohydroquinone in the Lamiaceae, and provide targets for metabolic engineering of high-value terpenes in plants., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Pancreatic adenocarcinoma (PAAD) is an extremely lethal disease worldwide. Brain-derived neurotrophic factor (BDNF) is a critical member of the neurotrophin polypeptide superfamily that plays an important role in multiple cancers. However, the association among BDNF expression, tumor immunity, and PAAD prognosis remains unclear. BDNF expression and its influence on patient prognosis were explored based on The Cancer Genome Atlas, Cancer Cell Line Encyclopedia, Genotype-Tissue Expression, and Kaplan-Meier plotter. Gene set enrichment analysis was performed to understand the biological roles of BDNF. The role of BDNF in tumor-infiltrating immune cells was determined using the Tumor Immune Estimation Resource database and the single-sample gene set enrichment analysis and xCell algorithm. The correlation among BDNF and chemokines, chemokine receptors, chemotherapeutic efficacy, and immune checkpoints was analyzed based on RStudio. BDNF expression was remarkably higher in PAAD compared to their paired normal tissues, and high BDNF expression was associated with unfavorable prognosis. Enrichment analysis revealed that BDNF was significantly enriched in major oncogenic pathways in PAAD. BDNF expression was positively correlated with immune infiltration, especially Th2 cells. Moreover, BDNF expression was positively correlated with Th2 cell-related chemokine/chemokine receptors, indicating that BDNF might modulate the migration of Th2 cells in PAAD. We also found that BDNF expression was correlated with high chemotherapeutics sensitivity and highly expressed immune checkpoints, making it a valuable biomarker in predicting the therapeutic benefits for chemotherapy and immunotherapy in cancer patients. In summary, BDNF might affect patient prognosis by interacting with tumor-infiltrating Th2 cells, thus serving as a potential prognostic biomarker in PAAD., Competing Interests: The authors declare that they have no conflicts of interest., (Copyright © 2021 Yanan Zhu et al.)

Colon adenocarcinoma (COAD) is one of the most common malignant tumors and has high migration and invasion capacity. In this study, we attempted to establish a multigene signature for predicting the prognosis of COAD patients. Weighted gene co-expression network analysis and differential gene expression analysis methods were first applied to identify differentially co-expressed genes between COAD tissues and normal tissues from the Cancer Genome Atlas (TCGA)-COAD dataset and GSE39582 dataset, and a total of 309 overlapping genes were screened out. Then, our study employed TCGA-COAD cohort as the training dataset and an independent cohort by merging the GES39582 and GSE17536 datasets as the testing dataset. After univariate and multivariate Cox regression analyses were performed for these overlapping genes and overall survival (OS) of COAD patients in the training dataset, a 13-gene signature was constructed to divide COAD patients into high- and low-risk subgroups with significantly different OS. The testing dataset exhibited the same results utilizing the same predictive signature. The area under the curve of receiver operating characteristic analysis for predicting OS in the training and testing datasets were 0.789 and 0.868, respectively, which revealed the enhanced predictive power of the signature. Multivariate Cox regression analysis further suggested that the 13-gene signature could independently predict OS. Among the 13 prognostic genes, NAT1 and NAT2 were downregulated with deep deletions in tumor tissues in multiple COAD cohorts and exhibited significant correlations with poorer OS based on the GEPIA database. Notably, NAT1 and NAT2 expression levels were positively correlated with infiltrating levels of CD8+ T cells and dendritic cells, exhibiting a foundation for further research investigating the antitumor immune roles played by NAT1 and NAT2 in COAD. Taken together, the results of our study showed that the 13-gene signature could efficiently predict OS and that NAT1 and NAT2 could function as biomarkers for prognosis and the immune response in COAD., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zhang, Zhao, Liu, Yao and Zhao.)

Aim: Long non-coding RNAs (lncRNAs) have been identified to regulate cancers by controlling the process of autophagy and by mediating the post-transcriptional and transcriptional regulation of autophagy-related genes. This study aimed to investigate the potential prognostic role of autophagy-associated lncRNAs in colorectal cancer (CRC) patients., Methods: LncRNA expression profiles and the corresponding clinical information of CRC patients were collected from The Cancer Genome Atlas (TCGA) database. Based on the TCGA dataset, autophagy-related lncRNAs were identified by Pearson correlation test. Univariate Cox regression analysis and the least absolute shrinkage and selection operator analysis (LASSO) Cox regression model were performed to construct the prognostic gene signature. Gene set enrichment analysis (GSEA) was used to further clarify the underlying molecular mechanisms., Results: We obtained 210 autophagy-related genes from the whole dataset and found 1187 lncRNAs that were correlated with the autophagy-related genes. Using Univariate and LASSO Cox regression analyses, eight lncRNAs were screened to establish an eight-lncRNA signature, based on which patients were divided into the low-risk and high-risk group. Patients' overall survival was found to be significantly worse in the high-risk group compared to that in the low-risk group (log-rank p = 2.731E-06). ROC analysis showed that this signature had better prognostic accuracy than TNM stage, as indicated by the area under the curve. Furthermore, GSEA demonstrated that this signature was involved in many cancer-related pathways, including TGF-β, p53, mTOR and WNT signaling pathway., Conclusions: Our study constructed a novel signature from eight autophagy-related lncRNAs to predict the overall survival of CRC, which could assistant clinicians in making individualized treatment.

Long non-coding RNAs (lncRNAs) were reported to have the potential in maintaining genome instability, but the identification of lncRNAs related to genome instability and their prognostic value have not been largely explored in colon cancer. In this study, we obtained 155 genome instability-associated lncRNAs based on somatic mutation profiles in colon cancer from The Cancer Genome Atlas (TCGA) database. Functional enrichment analysis revealed the possible roles of genes co-expressed with those lncRNAs involved in some cancer, genome instability and immune related biological processes. Combined with overall survival data, a seven-lncRNA signature was established for prognosis prediction. According to the risk score calculated by this signature, high-risk patients characterized by high somatic mutation count, high microsatellite instability, significantly poorer clinical outcomes and specific tumor immune infiltration status compared with low-risk patients. The lncRNA signature was validated to be an independent prognostic indicator with good predictive performance in TCGA cohort. Furthermore, the prognostic value of the ZNF503-AS1 in lncRNA signature was confirmed in another independent dataset from Gene Expression Omnibus database. In summary, the genome instability-associated lncRNA signature in this study could be a promising tool for effectively predicting survival outcomes in colon cancer., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Yin, Zhao and Yao.)

The treatment of asymptomatic hydronephrosis due to ureteropelvic junction obstruction (UPJO), as well as the timing and indications for surgical intervention, remain controversial. Diabetes insipidus (DI) is a rare disease in infants that is known to cause non-obstructive hydronephrosis, while its association with obstructive hydronephrosis has not been reported. Some studies have found that increased water intake is a predisposing risk factor of developing hydronephrosis. However, there are no studies or guidelines that indicate the specific follow-up intervals and surgical indications for mild hydronephrosis if predisposing risk factors persist. A 46-month-old boy was admitted to our Urology Department with a history of Society of Fetal Urology (SFU) Grade 2 prenatal left hydronephrosis, which was stable at SFU Grade 1-2 at regular postnatal follow-ups. The patient developed polydipsia and polyuria three months prior to admission, then he was considered as primary polydipsia by endocrinology and was treated with fluid restriction while the examination was negative. Renal ultrasound at follow-up demonstrated severe left hydronephrosis with an anterior-posterior diameter (APD) of 6.25 cm three months after symptom onset. Diuretic renography (DR) revealed a renal function of 13.7% with a glomerular filtration rate (GFR) of 11.25 mL/min. The patient was otherwise asymptomatic without any abdominal pain or vomiting. He underwent left pyelostomy immediately as well as laparoscopic left dismembered ureteropelvioplasty after three months, and a diagnosis of UPJO was confirmed. The patient had an uncomplicated postoperative recovery and the result of follow-up renal ultrasound was stable. However, the symptoms of polydipsia and polyuria did not improve significantly. He underwent pituitary magnetic resonance imaging (MRI) and pathological examination, the results of which were consistent with central DI caused by Langerhans cell hyperplasia four months postoperatively. This case indicates the need to pay attention to children with mild hydronephrosis undergoing regular observation and conservative treatment, as a sudden aggravation of the hydronephrosis and a rapid decline of renal function may occur if DI persists., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at http://dx.doi.org/10.21037/tp-20-476). The authors have no conflicts of interest to declare., (2021 Translational Pediatrics. All rights reserved.)

Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.

Objective: To investigate the clinicopathological and molecular features of colorectal cancer (CRC) with synchronous adenoma and to describe features of synchronous adenomas in CRC patients., Methods: Single-centre retrospective cohort of 180 patients were included. The clinicopathological and endoscopic data were collected. The expression mismatch repair (MMR) proteins were detected by immunohistochemistry. The determination of microsatellite instability (MSI) was performed by multiple fluorescence PCR, and the mutations of genes were detected by real-time PCR., Results: Among all cases, 49 were diagnosed as CRC with synchronous adenoma, and 131 were diagnosed as solitary CRC. Some of the differences between the groups are: higher incidence was found in male (71.4 vs. 52.6%, p  = .023) and in patients with habit drinking (34.7 vs. 14.5%, p  = .030) and with other neoplastic diseases (42.7 vs. 26%, p  = .028). Less tumors in the synchronous group were diagnosed as stage III and IV than in the solitary group (28.6 vs. 45%, p  = .045). One and four mutant subtypes of KRAS gene mutations were detected insynchronous group and solitary group respectively.The prevalence of BRAF mutations in solitary group was higher than that in the synchronous group (7.4 vs. 0%, p  = .045). A total of 123 adenomas were found in synchronous group and they tend to be smaller than 10 mm (74%)., Conclusion: Gender, a habit of drinking and other neoplastic diseases are risk factors for the development of a synchronous adenoma. With a low rate of BRAF mutations, the responses to monoclonal antibody and prognosis of patients with synchronous adenomas may be better than that of solitary CRC.

Grafting is a well-established agricultural practice in cherry production for clonal propagation, altered plant vigor and architecture, increased tolerance to biotic and abiotic stresses, precocity, and higher yield. Mobile molecules, such as water, hormones, nutrients, DNAs, RNAs, and proteins play essential roles in rootstock-scion interactions. Small RNAs (sRNAs) are 19 to 30-nucleotides (nt) RNA molecules that are a group of mobile signals in plants. Rootstock-to-scion transfer of transgene-derived small interfering RNAs enabled virus resistance in nontransgenic sweet cherry scion. To determine whether there was long-distance scion-to-rootstock transfer of endogenous sRNAs, we compared sRNAs profiles in bud tissues of an ungrafted 'Gisela 6' rootstock, two sweet cherry 'Emperor Francis' scions as well as their 'Gisela 6' rootstocks. Over two million sRNAs were detected in each sweet cherry scion, where 21-nt sRNA (56.1% and 55.8%) being the most abundant, followed by 24-nt sRNAs (13.1% and 12.5%). Furthermore, we identified over three thousand sRNAs that were potentially transferred from the sweet cherry scions to their corresponding rootstocks. In contrast to the sRNAs in scions, among the transferred sRNAs in rootstocks, the most abundant were 24-nt sRNAs (46.3% and 34.8%) followed by 21-nt sRNAs (14.6% and 19.3%). In other words, 21-nt sRNAs had the least transferred proportion out of the total sRNAs in sources (scions) while 24-nt had the largest proportion. The transferred sRNAs were from 574 cherry transcripts, of which 350 had a match from the Arabidopsis thaliana standard protein set. The finding that "DNA or RNA binding activity" was enriched in the transcripts producing transferred sRNAs indicated that they may affect the biological processes of the rootstocks at different regulatory levels. Overall, the profiles of the transported sRNAs and their annotations revealed in this study facilitate a better understanding of the role of the long-distance transported sRNAs in sweet cherry rootstock-scion interactions as well as in branch-to-branch interactions in a tree., Competing Interests: The authors have declared that no competing interests exist.

Catnip or catmint ( Nepeta spp.) is a flowering plant in the mint family (Lamiaceae) famed for its ability to attract cats. This phenomenon is caused by the compound nepetalactone, a volatile iridoid that also repels insects. Iridoids are present in many Lamiaceae species but were lost in the ancestor of the Nepetoideae, the subfamily containing Nepeta . Using comparative genomics, ancestral sequence reconstructions, and phylogenetic analyses, we probed the re-emergence of iridoid biosynthesis in Nepeta . The results of these investigations revealed mechanisms for the loss and subsequent re-evolution of iridoid biosynthesis in the Nepeta lineage. We present evidence for a chronology of events that led to the formation of nepetalactone biosynthesis and its metabolic gene cluster. This study provides insights into the interplay between enzyme and genome evolution in the origins, loss, and re-emergence of plant chemical diversity., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to more than 100 countries. Children approved to be susceptible to SARS-CoV-2 infection. Preventing and controlling the epidemic while ensuring orderly flows of pediatric surgery clinical work has proven to be a big challenge for both patients and clinicians during the epidemic. Based on the transmission characteristics of SARS-CoV-2 and the requirements for prevention and control of COVID-19, the authors proposed some concrete measures and practical strategies of managing emergency, limited-term, and elective pediatric surgeries during the epidemic period., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

In this work, magnetic CuFe 2 O 4 /Ag nanoparticles activated by porous covalent organic frameworks (COF) was fabricated to evaluate the heterogenous reduction of 4-nitrophenol (4-NP). The core-shell CuFe 2 O 4 /Ag@COF was successfully prepared by polydopamine reduction of silver ions on CuFe 2 O 4 nanoparticles, followed by COF layer condensation. By integrating the intrinsic characteristics of the magnetic CuFe 2 O 4 /Ag core and COF layer, the obtained nanocomposite exhibited features of high specific surface area (464.21 m 2 g -1 ), ordered mesoporous structure, strong environment stability, as well as fast magnetic response. Accordingly, the CuFe 2 O 4 /Ag@COF catalyst showed good affinity towards 4-NP via π-π stacking interactions and possessed enhanced catalytic activity compared with CuFe 2 O 4 /Ag and CuFe 2 O 4 @COF. The pseudo-first-order rate constant of CuFe 2 O 4 /Ag@COF (0.77 min -1 ) is 3 and 5 times higher than CuFe 2 O 4 /Ag and CuFe 2 O 4 @COF, respectively. The characteristics of bi-catalytic CuFe 2 O 4 /Ag and the porous COF shell of CuFe 2 O 4 /Ag@COF made a contribution to improve the activity of 4-NP reduction. The present work demonstrated a facile strategy to fabricate COF-activated nano-catalysts with enhanced performance in the fields of nitrophenolic wastewater treatment.

A facile approach was successfully developed for synthesis of cellulose nanocrystals (CNC)-supported magnetic CuFe 2 O 4 @Ag@ZIF-8 nanospheres which consist of a paramagnetic CuFe 2 O 4 @Ag core and porous ZIF-8 shell. The CuFe 2 O 4 nanoparticles (NPs) were first prepared in the presence of CNC and dispersant. Ag NPs were then deposited on the CuFe 2 O 4 /CNC composites via an in situ reduction directed by dopamine polymerization (PDA). The CuFe 2 O 4 /CNC@Ag@ZIF-8 nanocomposite was characterized by TEM, FTIR, XRD, N 2 adsorption-desorption isotherms, VSM, and XPS. Catalytic studies showed that the CuFe 2 O 4 /CNC@Ag@ZIF-8 catalyst had much higher catalytic activity than CuFe 2 O 4 @Ag catalyst with the rate constant of 0.64 min -1 . Because of the integration of ZIF-8 with CuFe 2 O 4 /CNC@Ag that combines the advantaged of each component, the nanocomposites were demonstrated to have an enhanced catalytic activity in heterogeneous catalysis. Therefore, these results demonstrate a new method for the fabrication of CNC-supported magnetic core-shell catalysts, which display great potential for application in biocatalysis and environmental chemistry.

Background: Teak, a member of the Lamiaceae family, produces one of the most expensive hardwoods in the world. High demand coupled with deforestation have caused a decrease in natural teak forests, and future supplies will be reliant on teak plantations. Hence, selection of teak tree varieties for clonal propagation with superior growth performance is of great importance, and access to high-quality genetic and genomic resources can accelerate the selection process by identifying genes underlying desired traits., Findings: To facilitate teak research and variety improvement, we generated a highly contiguous, chromosomal-scale genome assembly using high-coverage Pacific Biosciences long reads coupled with high-throughput chromatin conformation capture. Of the 18 teak chromosomes, we generated 17 near-complete pseudomolecules with one chromosome present as two chromosome arm scaffolds. Genome annotation yielded 31,168 genes encoding 46,826 gene models, of which, 39,930 and 41,155 had Pfam domain and expression evidence, respectively. We identified 14 clusters of tandem-duplicated terpene synthases (TPSs), genes central to the biosynthesis of terpenes, which are involved in plant defense and pollinator attraction. Transcriptome analysis revealed 10 TPSs highly expressed in woody tissues, of which, 8 were in tandem, revealing the importance of resolving tandemly duplicated genes and the quality of the assembly and annotation. We also validated the enzymatic activity of four TPSs to demonstrate the function of key TPSs., Conclusions: In summary, this high-quality chromosomal-scale assembly and functional annotation of the teak genome will facilitate the discovery of candidate genes related to traits critical for sustainable production of teak and for anti-insecticidal natural products., (© The Author(s) 2019. Published by Oxford University Press.)

Genome mining is a routine technique in microbes for discovering biosynthetic pathways. In plants, however, genomic information is not commonly used to identify novel biosynthesis genes. Here, we present the genome of the medicinal plant and oxindole monoterpene indole alkaloid (MIA) producer Gelsemium sempervirens (Gelsemiaceae). A gene cluster from Catharanthus roseus, which is utilized at least six enzymatic steps downstream from the last common intermediate shared between the two plant alkaloid types, is found in G. sempervirens, although the corresponding enzymes act on entirely different substrates. This study provides insights into the common genomic context of MIA pathways and is an important milestone in the further elucidation of the Gelsemium oxindole alkaloid pathway., (© 2019 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Acquisition and rearrangement of host genes by transposable elements (TEs) is an important mechanism to increase gene diversity as exemplified by the ∼3000 Pack-Mutator-like TEs in the rice genome which have acquired gene sequences (Pack-MULEs), yet remain enigmatic. To identify signatures of functioning Pack-MULEs and Pack-MULE evolution, we generated transcriptome, translatome, and epigenome datasets and compared Pack-MULEs to genes and other TE families. Approximately 40% of Pack-MULEs were transcribed with 9% having translation evidence, clearly distinguishing them from other TEs. Pack-MULEs exhibited a unique expression profile associated with specificity in reproductive tissues that may be associated with seed traits. Expressed Pack-MULEs resemble regular protein-coding genes as exhibited by a low level of DNA methylation, association with active histone marks and DNase I hypersensitive sites, and an absence of repressive histone marks, suggesting that a substantial fraction of Pack-MULEs are potentially functional in vivo. Interestingly, the expression capacity of Pack-MULEs is independent of the local genomic environment, and the insertion and expression of Pack-MULEs may have altered the local chromosomal expression pattern as well as counteracted the impact of recombination on chromosomal base composition, which has profound consequences on the evolution of chromosome structure.

Calotropis gigantea produces specialized secondary metabolites known as cardenolides, which have anticancer and antimalarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high-quality de novo assembly was generated for C. gigantea , representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome data in the form of RNA-sequencing libraries from a developmental tissue series was generated to aid the annotation and construction of a gene expression atlas. Using an ab initio and evidence-driven gene annotation pipeline, 18,197 high-confidence genes were annotated. Homologous and syntenic relationships between C. gigantea and other species within the Apocynaceae family confirmed previously identified evolutionary relationships, and suggest the emergence or loss of the specialized cardenolide metabolites after the divergence of the Apocynaceae subfamilies. The C. gigantea genome assembly, annotation, and RNA-sequencing data provide a novel resource to study the cardenolide biosynthesis pathway, especially for understanding the evolutionary origin of cardenolides and the engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications., (Copyright © 2018 Hoopes et al.)

Nepetalactones are iridoid monoterpenes with a broad range of biological activities produced by plants in the Nepeta genus. However, none of the genes for nepetalactone biosynthesis have been discovered. Here we report the transcriptomes of two Nepeta species, each with distinctive profiles of nepetalactone stereoisomers. As a starting point for investigation of nepetalactone biosynthesis in Nepeta, these transcriptomes were used to identify candidate genes for iridoid synthase homologs, an enzyme that has been shown to form the core iridoid skeleton in several iridoid producing plant species. Iridoid synthase homologs identified from the transcriptomes were cloned, heterologously expressed, and then assayed with the 8-oxogeranial substrate. These experiments revealed that catalytically active iridoid synthase enzymes are present in Nepeta, though there are unusual mutations in key active site residues. Nevertheless, these enzymes exhibit similar catalytic activity and product profile compared to previously reported iridoid synthases from other plants. Notably, four nepetalactone stereoisomers with differing stereochemistry at the 4α and 7α positions - which are generated during the iridoid synthase reaction - are observed at different ratios in various Nepeta species. This work strongly suggests that the variable stereochemistry at these 4α and 7α positions of nepetalactone diastereomers is established further downstream in the iridoid pathway in Nepeta. Overall, this work provides a gateway into the biosynthesis of nepetalactones in Nepeta., (Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Rationale: Efficient elimination of pathogenic bacteria is a critical determinant in the outcome of sepsis. Sphingosine-1-phosphate receptor 3 (S1PR3) mediates multiple aspects of the inflammatory response during sepsis, but whether S1PR3 signaling is necessary for eliminating the invading pathogens remains unknown., Objectives: To investigate the role of S1PR3 in antibacterial immunity during sepsis., Methods: Loss- and gain-of-function experiments were performed using cell and murine models. S1PR3 levels were determined in patients with sepsis and healthy volunteers., Measurements and Main Results: S1PR3 protein levels were up-regulated in macrophages upon bacterial stimulation. S1pr3 -/- mice showed increased mortality and increased bacterial burden in multiple models of sepsis. The transfer of wild-type bone marrow-derived macrophages rescued S1pr3 -/- mice from lethal sepsis. S1PR3-overexpressing macrophages further ameliorated the mortality rate of sepsis. Loss of S1PR3 led to markedly decreased bacterial killing in macrophages. Enhancing endogenous S1PR3 activity using a peptide agonist potentiated the macrophage bactericidal function and improved survival rates in multiple models of sepsis. Mechanically, the reactive oxygen species levels were decreased and phagosome maturation was delayed in S1pr3 -/- macrophages due to impaired recruitment of vacuolar protein-sorting 34 to the phagosomes. In addition, S1RP3 expression levels were elevated in monocytes from patients with sepsis. Higher levels of monocytic S1PR3 were associated with efficient intracellular bactericidal activity, better immune status, and preferable outcomes., Conclusions: S1PR3 signaling drives bacterial killing and is essential for survival in bacterial sepsis. Interventions targeting S1PR3 signaling could have translational implications for manipulating the innate immune response to combat pathogens.

The high-nuclearity polyoxovanadate-based carboxylate derivative K 6 H[V V 17 V IV 12 (OH) 4 O 60 (OOC(CH 2 ) 4 COO) 8 ]·nH 2 O (1) has been successfully synthesized by conventional aqueous methods and structurally characterized. The [V V 17 V IV 12 (OH) 4 O 60 (OOC(CH 2 ) 4 COO) 8 ] 7- polyanion is built up from three cages: one {V V 17 (OH) 4 O 44 } cage and two identical [(V IV 3 O 6 ) 2 (OOC(CH 2 ) 4 COO) 4 ] 8- cages. Of the three cages, the {V V 17 (OH) 4 O 44 } is a purely inorganic polyoxovanadate cluster, whereas each of the [(V IV 3 O 6 ) 2 (OOC(CH 2 ) 4 COO) 4 ] 8- cages is a vanadium-based organic-inorganic hybrid cluster framed via four adipate ligands linking simultaneously to two triangular {V 3 } units. The two [(V IV 3 O 6 ) 2 (OOC(CH 2 ) 4 COO) 4 ] 8- cages are covalently attached to the central {V V 17 (OH) 4 O 44 } cage via V-O-V bonds in a linear arrangement, resulting in a {V 29 }-based hybrid cluster skeleton. The catalytic properties of compound 1 for the oxidation of sulfides by tert-butyl hydroperoxide were investigated, and the result indicates that 1 exhibits excellent catalytic activity for the oxidation of sulfides under mild conditions.