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Copy number variation (CNV) is a class of key biomarkers in many complex traits and diseases. Detecting CNV from sequencing data is a substantial bioinformatics problem and a standard requirement in clinical practice. Although many proposed CNV detection approaches exist, the core statistical model at their foundation is weakened by two critical computational issues: (i) identifying the optimal setting on the sliding window and (ii) correcting for bias and noise. We designed a statistical process model to overcome these limitations by calculating regional read depths via an exponentially weighted moving average strategy. A one-run detection of CNVs of various lengths is then achieved by a dynamic sliding window, whose size is self-adopted according to the weighted averages. We also designed a novel bias/noise reduction model, accompanied by the moving average, which can handle complicated patterns and extend training data. This model, called PEcnv, accurately detects CNVs ranging from kb-scale to chromosome-arm level. The model performance was validated with simulation samples and real samples. Comparative analysis showed that PEcnv outperforms current popular approaches. Notably, PEcnv provided considerable advantages in detecting small CNVs (1 kb-1 Mb) in panel sequencing data. Thus, PEcnv fills the gap left by existing methods focusing on large CNVs. PEcnv may have broad applications in clinical testing where panel sequencing is the dominant strategy. Availability and implementation: Source code is freely available at https://github.com/Sherwin-xjtu/PEcnv.
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Variaciones en el Número de Copia de ADN , Secuenciación de Nucleótidos de Alto Rendimiento , Algoritmos , Biología Computacional/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Programas InformáticosRESUMEN
The Pseudoalteromonas genus marine bacteria have attracted increasing interest because of their abilities to produce bioactive metabolites. The pigmented Pseudoalteromonas group encodes more secondary metabolite biosynthetic gene clusters (BGCs) than the non-pigmented group. Here, we report a yellow pigmented bacterium Pseudoalteromonas sp. strain T1lg65, which was isolated from a mangrove forest sediment. We showed that the yellow pigments of T1lg65 belong to the group of lipopeptide alterochromides. Further genetic analyses of the alterochromide BGC revealed that the yellow pigments are biosynthesized by aryl-polyene synthases and nonribosomal peptide synthases. Within the gene cluster, altA encodes a tyrosine ammonia acid lyase, which catalyzes synthesis of the precursor 4-hydroxycinnamic acid (4-HCA) from tyrosine in the alterochromide biosynthetic pathway. In addition, altN, encoding a putative flavin-dependent halogenase, was proven to be responsible for the bromination of alterochromides based on gene deletion, molecular docking, and site mutagenesis analyses. In summary, the biosynthetic pathway, precursor synthesis, and bromination mechanism of the lipopeptide alterochromides were studied in-depth. Our results expand the knowledge on biosynthesis of Pseudoalteromonas pigments and could promote the development of active pigments in the future.IMPORTANCEThe marine bacteria Pseudoalteromonas spp. are important biological resources because they are producers of bioactive natural products, including antibiotics, pigments, enzymes, and antimicrobial peptides. One group of the microbial pigments, alterochromides, holds a great value for their novel lipopeptide structures and antimicrobial activities. Previous studies were limited to the structural characterization of alterochromides and genome mining for the alterochromide biosynthesis. This work focused on the biosynthetic mechanism for alterochromide production, especially revealing functions of two key genes within the gene cluster for the alterochromide biosynthesis. On the one hand, our study provides a target for metabolic engineering of the alterochromide biosynthesis; on the other hand, the 4-HCA synthase AltA and brominase AltN show potential in the biocatalyst industry.
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Pseudoalteromonas , Pseudoalteromonas/genética , Pseudoalteromonas/metabolismo , Simulación del Acoplamiento Molecular , Flavinas/metabolismo , Lipopéptidos/metabolismo , Tirosina/metabolismoRESUMEN
PURPOSE: The purpose of this study was to explore the expression and potential mechanism of hsa_circ_0005397 in hepatocellular carcinoma progression. METHODS: Quantitative reverse transcription-polymerase chain reaction(qRT-PCR) was used to measure the expression level of hsa_circ_0005397 and EIF4A3 from paired HCC tissues and cell lines. Western Blot (WB) and immunohistochemistry (IHC) were used to verify the protein level of EIF4A3. The specificity of primers was confirmed by agarose gel electrophoresis. Receiver Operating Characteristic (ROC) Curve was drawn to analyze diagnostic value. Actinomycin D and nuclear and cytoplasmic extraction assays were utilized to evaluate the characteristics of hsa_circ_0005397. Cell Counting kit-8 (CCK-8) and colony formation assays were performed to detect cell proliferation. Flow cytometry analysis was used to detect the cell cycle. Transwell assay was performed to determine migration and invasion ability. RNA-binding proteins (RBPs) of hsa_circ_0005397 in HCC were explored using bioinformatics websites. The relationship between hsa_circ_0005397 and Eukaryotic Translation Initiation Factor 4A3 (EIF4A3) was verified by RNA Binding Protein Immunoprecipitation (RIP) assays, correlation and rescue experiments. RESULTS: In this study, hsa_circ_0005397 was found to be significantly upregulated in HCC, and the good diagnostic sensitivity and specificity shown a potential diagnostic capability. Upregulated expression of hsa_circ_0005397 was significantly related to tumor size and stage. Hsa_circ_0005397 was circular structure which more stable than liner mRNA, and mostly distributed in the cytoplasm. Upregulation of hsa_circ_0005397 generally resulted in stronger proliferative ability, clonality, and metastatic potency of HCC cells; its downregulation yielded the opposite results. EIF4A3 is an RNA-binding protein of hsa_circ_0005397, which overexpressed in paired HCC tissues and cell lines. In addition, expression of hsa_circ_0005397 decreased equally when EIF4A3 was depleted. RIP assays and correlation assay estimated that EIF4A3 could interacted with hsa_circ_0005397. Knockdown of EIF4A3 could reverse hsa_circ_0005397 function in HCC progression. CONCLUSIONS: Hsa_circ_0005397 promotes progression of hepatocellular carcinoma through EIF4A3. These research findings may provide novel clinical value for hepatocellular carcinoma.
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Carcinoma Hepatocelular , Neoplasias Hepáticas , MicroARNs , Humanos , Carcinoma Hepatocelular/patología , Neoplasias Hepáticas/patología , ARN Circular/genética , ARN Circular/metabolismo , Regulación hacia Abajo , Línea Celular Tumoral , Proliferación Celular/genética , Regulación Neoplásica de la Expresión Génica , MicroARNs/genética , Factor 4A Eucariótico de Iniciación/genética , Factor 4A Eucariótico de Iniciación/metabolismo , ARN Helicasas DEAD-box/genéticaRESUMEN
BACKGROUND: Recently, dynamic contrast-enhanced (DCE) MRI with ferumoxytol as contrast agent has recently been introduced for the noninvasive assessment of placental structure and function throughout. However, it has not been demonstrated under pathological conditions. PURPOSE: To measure cotyledon-specific rhesus macaque maternal placental blood flow using ferumoxytol DCE MRI in a novel animal model for local placental injury. STUDY TYPE: Prospective animal model. SUBJECTS: Placental injections of Tisseel (three with 0.5 mL and two with 1.5 mL), monocyte chemoattractant protein 1 (three with 100 µg), and three with saline as controls were performed in a total of 11 rhesus macaque pregnancies at approximate gestational day (GD 101). DCE MRI scans were performed prior (GD 100) and after (GD 115 and GD 145) the injection (term = GD 165). FIELD STRENGTH/SEQUENCE: 3 T, T1-weighted spoiled gradient echo sequence (product sequence, DISCO). ASSESSMENT: Source images were inspected for motion artefacts from the mother or fetus. Placenta segmentation and DCE processing were performed for the dynamic image series to measure cotyledon specific volume, flow, and normalized flow. Overall placental histopathology was conducted for controls, Tisseel, and MCP-1 animals and regions of tissue infarctions and necrosis were documented. Visual inspections for potential necrotic tissue were conducted for the two Tisseelx3 animals. STATISTICAL TESTS: Wilcoxon rank sum test, significance level P < 0.05. RESULTS: No motion artefacts were observed. For the group treated with 1.5 mL of Tisseel, significantly lower cotyledon volume, flow, and normalized flow per cotyledon were observed for the third gestational time point of imaging (day ~145), with mean normalized flow of 0.53 minute-1 . Preliminary histopathological analysis shows areas of tissue necrosis from a selected cotyledon in one Tisseel-treated (single dose) animal and both Tisseelx3 (triple dose) animals. DATA CONCLUSION: This study demonstrates the feasibility of cotyledon-specific functional analysis at multiple gestational time points and injury detection in a placental rhesus macaque model through ferumoxytol-enhanced DCE MRI. LEVEL OF EVIDENCE: NA TECHNICAL EFFICACY: Stage 2.
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Pituitary adenomas (PAs) can exert pressure on the optic apparatus, leading to visual impairment. A subset of patients may observe a swift improvement in their vision following surgery. Nevertheless, the alterations in the structural connectome during the early postoperative period remain largely unexplored. The research employed probabilistic tractography, graph theoretical analysis, and statistical methods on preoperative and postoperative structural magnetic resonance imaging and diffusion tensor images from 13 PA patients. Postoperative analysis revealed an increase in global and local efficiency, signifying improved network capacity for parallel information transfer and fault tolerance, respectively. Enhanced clustering coefficient and reduced shortest path length were also observed, suggesting a more regular network organization and shortened communication steps within the brain network. Furthermore, alterations in node graphical properties were detected, implying a restructuring of the network's control points, possibly contributing to more efficient visual processing. These findings propose that rapid vision recovery post-surgery may be associated with significant reorganization of the brain's structural connectome, enhancing the efficiency and adaptability of the network, thereby facilitating improved visual processing.
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Conectoma , Neoplasias Hipofisarias , Humanos , Conectoma/métodos , Imagen de Difusión Tensora/métodos , Neoplasias Hipofisarias/diagnóstico por imagen , Neoplasias Hipofisarias/cirugía , Neoplasias Hipofisarias/complicaciones , Encéfalo/patología , Imagen por Resonancia Magnética/métodosRESUMEN
Hadal environments (depths below 6,000 m) are characterized by extremely high hydrostatic pressures, low temperatures, a scarce food supply, and little light. The evolutionary adaptations that allow vertebrates to survive in this extreme environment are poorly understood. Here, we constructed a high-quality reference genome for Yap hadal snailfish (YHS), which was captured at a depth of ~7,000 m in the Yap Trench. The final YHS genome assembly was 731.75 Mb, with a contig N50 of 0.75 Mb and a scaffold N50 of 1.26 Mb. We predicted 24,329 protein-coding genes in the YHS genome, and 24,265 of these genes were successfully functionally annotated. Phylogenetic analyses suggested that YHS diverged from a Mariana Trench snailfish approximately 0.92 million years ago. Many genes associated with DNA repair show evidence of positive selection and have expanded copy numbers in the YHS genome, possibly helping to maintain the integrity of DNA under increased hydrostatic pressure. The levels of trimethylamine N-oxide (TMAO), a potent protein stabilizer, are much higher in the muscles of YHS than in those of shallow-water fish. This difference is perhaps due to the five copies of the TMAO-generating enzyme flavin-containing monooxygenase-3 gene (fmo3) in the YHS genome and the abundance of trimethylamine (TMA)-generating bacteria in the YHS gut. Thus, the high TMAO content might help YHS adapt to high hydrostatic pressure by improving protein stability. Additionally, the evolutionary features of the YHS genes encoding sensory-related proteins are consistent with the scarce food supply and darkness in the hadal environments. These results clarify the molecular mechanisms underlying the adaptation of hadal organisms to the deep-sea environment and provide valuable genomic resources for in-depth investigations of hadal biology.
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Aclimatación/genética , Ambientes Extremos , Peces/genética , Genoma/genética , Océanos y Mares , Secuenciación Completa del Genoma , Animales , Reparación del ADN/genética , Oscuridad , Evolución Molecular , Peces/clasificación , Presión Hidrostática , Metilaminas/metabolismo , Oxigenasas/genética , Oxigenasas/metabolismo , Filogenia , Estabilidad ProteicaRESUMEN
BACKGROUND: Alzheimer's disease (AD), Parkinson's disease (PD), and multiple sclerosis (MS) are three nervous system diseases that partially overlap clinically and genetically. However, bulk RNA-sequencing did not accurately detect the core pathogenic molecules in them. The availability of high-quality single cell RNA-sequencing data of post-mortem brain collections permits the generation of a large-scale gene expression in different cells in human brain, focusing on the molecular features and relationships between diseases and genes. We integrated single-nucleus RNA-sequencing (snRNA-seq) datasets of human brains with AD, PD, and MS to identify transcriptomic commonalities and distinctions among them. METHODS: The snRNA-seq datasets were downloaded from Gene Expression Omnibus (GEO) database. The Seurat package was used for snRNA-seq data processing. The uniform manifold approximation and projection (UMAP) were utilized for cluster identification. The FindMarker function in Seurat was used to identify the differently expressed genes. Functional enrichment analysis was carried out using the Gene Set Enrichment Analysis (GSEA) and Gene ontology (GO). The protein-protein interaction (PPI) analysis of differentially expressed genes (DEGs) was analyzed using STRING database ( http://string-db.org ). SCENIC analysis was performed using utilizing pySCENIC (v0.10.0) based on the hg19-tss-centered-10 kb-10species databases. The analysis of potential therapeutic drugs was analyzed on Connectivity Map ( https://clue.io ). RESULTS: The gene regulatory network analysis identified several hub genes regulated in AD, PD, and MS, in which HSPB1 and HSPA1A were key molecules. These upregulated HSP family genes interact with ribosome genes in AD and MS, and with immunomodulatory genes in PD. We further identified several transcriptional regulators (SPI1, CEBPA, TFE3, GRHPR, and TP53) of the hub genes, which has important implications for uncovering the molecular crosstalk among AD, PD, and MS. Arctigenin was identified as a potential therapeutic drug for AD, PD, and MS. CONCLUSIONS: Together, the integrated snRNA-seq data and findings have significant implications for unraveling the shared and unique molecular crosstalk among AD, PD, and MS. HSPB1 and HSPA1A as promising targets involved in the pathological mechanisms of neurodegenerative diseases. Additionally, the identification of arctigenin as a potential therapeutic drug for AD, PD, and MS further highlights its potential in treating these neurological disorders. These discoveries lay the groundwork for future research and interventions to enhance our understanding and treatment of AD, PD, and MS.
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Enfermedad de Alzheimer , Esclerosis Múltiple , Enfermedad de Parkinson , Humanos , Enfermedad de Parkinson/genética , Esclerosis Múltiple/genética , Enfermedad de Alzheimer/genética , ARNRESUMEN
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) stands as one of the pivotal afforestation tree species and timber resources in southern China. Nevertheless, the occurrence of seed abortion and a notably high proportion of astringent seeds significantly curtail the yield and quality of elite seeds, resulting in substantial economic losses. The development of astringent seeds is accompanied by significant physiological and biochemical alterations. Here, the first combined lipidomic and metabolomic analysis was performed to gain a comprehensive understanding of astringent seed traits. A total of 744 metabolites and 616 lipids were detected, of which 489 differential metabolites and 101 differential lipids were identified. In astringent seeds, most flavonoids and tannins, as well as proline and γ-aminobutyric acid, were more accumulated, along with a notable decrease in lipid unsaturation, indicating oxidative stress in the cells of astringent seeds. Conversely, numerous elemental metabolites were less accumulated, including amino acids and their derivatives, saccharides and alcohols, organic acids and nucleotides and their derivatives. Meanwhile, most lipid subclasses, mainly associated with energy storage (triglyceride and diglyceride) and cell membrane composition (phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine), also exhibited significant reductions. These results reflected a disruption in the cellular system or the occurrence of cell death, causing a reduction in viable cells within astringent seeds. Furthermore, only one lipid subclass, sphingosine phosphate (SoP), was more accumulated in astringent seeds. Additionally, lower accumulation of indole-3-acetic acid and more accumulation of salicylic acid (SA) were also identified in astringent seeds. Both SA and SoP were closely associated with the promotion of programmed cell death in astringent seeds. Collectively, our study revealed significant abnormal changes in phytohormones, lipids and various metabolites in astringent seeds, allowing us to propose a model for the development of astringent seeds in Chinese fir based on existing research and our findings. This work enriches our comprehension of astringent seeds and presents valuable bioindicators for the identification of astringent seeds.
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Cunninghamia , Cunninghamia/metabolismo , Astringentes/metabolismo , Lipidómica , Semillas , LípidosRESUMEN
As an effective immunostimulant, Astragalus polysaccharides (APS) have been widely used in fish aquaculture, however, their action mechanisms remain poorly understood. In the present paper, the inflammatory macrophage model of large yellow croaker (Larimichthys crocea) was constructed by using formalin-inactivated Vibrio alginolyticus. Inactivated V. alginolyticus could cause cellular damage of primary head kidney macrophages (PKM) by decreasing cell activity and inducing reactive oxygen species (ROS) production and cell apoptosis. When PKM were pretreated with APS, the depressed cell activity induced by inactivated V. alginolyticus was significantly improved, and ROS overproduction and cell apoptosis were inhibited. Then the protection mechanism of APS was investigated by transcriptome analysis. After treated with inactivated V. alginolyticus, the expression of immune-related genes (TLR5s, TLR13, Clec4e, IKK, IκB, BCL-3, NF-κB2, REL, IL-1ß, and IL-6) and pyroptosis-related genes (caspase-1, NLRP3, and NLRC3) in PKM were significantly up-regulated. However, APS pretreatment reversed the up-regulation of most of the above-mentioned genes, where TLR5s, BCL-3, REL, caspase-1, NLRP12, IL-1ß, and IL-6 were significantly down-regulated compared with inactivated V. alginolyticus-treated group. These results suggested that APS could protect large yellow croaker PKM against inactivated V. alginolyticus-induced inflammatory injury, and may exert their protection effects by activating NF-κB and pyroptosis signaling pathways. These findings therefore advance our understanding of the immune regulation mechanism of APS in fish, and facilitate the application of APS in prevention and control of fish bacteriosis.
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Enfermedades de los Peces , Perciformes , Animales , Vibrio alginolyticus/fisiología , Proteínas de Peces , Especies Reactivas de Oxígeno/metabolismo , Interleucina-6/metabolismo , Macrófagos , Polisacáridos/metabolismo , Caspasas/metabolismoRESUMEN
Dual-comb ranging (DCR) is an important method in absolute distance ranging because of its high precision, fast acquisition rate, and large measuring range. DCR needs to obtain precise results during distance measurements for a mobile target. However, the non-ambiguity range (NAR) is a challenge when pushing the dual-comb ranging to the industry field. This paper presents a solution for extending NAR by designing an algorithm and realizing it on a field-programmable gate array (FPGA). The algorithm is robust when facing the timing jitter in the optical frequency comb. Without averaging, the Allan deviation of the results in 1 ms is â¼3.89 µm and the Allan deviation of the results is â¼0.37 µm at an averaging time of 100 ms when the target object is standstill near the NAR. In addition, several ranging experiments were conducted on a mobile target whose speed was from â¼5 mm/s to â¼10 mm/s. The experimental results verify the effectiveness and robustness of our design. The implemented design is an online and real-time data processing unit that shows great industrial potential for using the DCR system.
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BACKGROUND: The misestimation of surgical risk is a serious threat to the lives of patients when implementing surgical risk calculator. Improving the accuracy of postoperative risk prediction has received much attention and many methods have been proposed to cope with this problem in the past decades. However, those linear approaches are inable to capture the non-linear interactions between risk factors, which have been proved to play an important role in the complex physiology of the human body, and thus may attenuate the performance of surgical risk calculators. METHODS: In this paper, we presented a new surgical risk calculator based on a non-linear ensemble algorithm named Gradient Boosting Decision Tree (GBDT) model, and explored the corresponding pipeline to support it. In order to improve the practicability of our approach, we designed three different modes to deal with different data situations. Meanwhile, considering that one of the obstacles to clinical acceptance of surgical risk calculators was that the model was too complex to be used in practice, we reduced the number of input risk factors according to the importance of them in GBDT. In addition, we also built some baseline models and similar models to compare with our approach. RESULTS: The data we used was three-year clinical data from Surgical Outcome Monitoring and Improvement Program (SOMIP) launched by the Hospital Authority of Hong Kong. In all experiments our approach shows excellent performance, among which the best result of area under curve (AUC), Hosmer-Lemeshow test ([Formula: see text]) and brier score (BS) can reach 0.902, 7.398 and 0.047 respectively. After feature reduction, the best result of AUC, [Formula: see text] and BS of our approach can still be maintained at 0.894, 7.638 and 0.060, respectively. In addition, we also performed multiple groups of comparative experiments. The results show that our approach has a stable advantage in each evaluation indicator. CONCLUSIONS: The experimental results demonstrate that NL-SRC can not only improve the accuracy of predicting the surgical risk of patients, but also effectively capture important risk factors and their interactions. Meanwhile, it also has excellent performance on the mixed data from multiple surgical fields.
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Algoritmos , Área Bajo la Curva , Hong Kong , Humanos , Medición de Riesgo , Factores de RiesgoRESUMEN
In this work, the removal of ammonia nitrogen and phenol by pulsed discharge plasma (PDP) and modified zeolite was investigated. The Fe-zeolite and Mn-zeolite catalysts were prepared by the impregnation method. Catalysts' morphology, specific surface area, and chemical bond structure were characterized. Based on the pollutants removal experiments, Fe-zeolite (0.01) in the PDP system had better catalytic oxidation of phenol and adsorption effect of ammonia nitrogen. The removal efficiency of the pollutants increased with the increase of discharge voltage and solution conductivity, but decreased with the increase of discharge distance. During the plasma discharge process, the pH value in the solution decreased, and the solution conductivity gradually increased. After PDP/Fe-zeolite system treatment, the toxicity of the wastewater was significantly reduced. This study provided a new treatment method for inorganic and organic pollutants treated by PDP.
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Contaminantes Químicos del Agua , Zeolitas , Amoníaco , Nitrógeno , Fenol , Fenoles , Contaminantes Químicos del Agua/análisisRESUMEN
A series of highly active MnO2@REOx (RE = Gd, Sm, Ce, and La) catalysts were successfully synthesized via in situ growth on the surface of MnO2, wherein the rare earth oxides were planted on the defect sites left by hydrogen peroxide etching of the surface of MnO2. Their physicochemical performance was investigated by scanning electron microscopy with energy-dispersive spectroscopy (SEM-EDS), X-ray diffraction (XRD), N2 adsorption-desorption, X-ray photoelectron spectroscopy (XPS), temperature-programmed reduction with hydrogen (H2-TPR), and temperature-programmed desorption of oxygen (O2-TPD). The catalytic properties are compared through the catalytic oxidation of chlorobenzene. Among all catalysts, MnO2@GdOx showed better mobility of surface lattice oxygen and higher molar ratios of Mn4+/Mn3+ (1.10) and Oads/Olatt (0.45), which promoted the superior low-temperature catalytic activity for chlorobenzene oxidation. The long-term chlorobenzene oxidation test (18 h) at different temperatures and the experiments with a mixture of VOCs showed that the as-prepared catalyst not only possessed a high stability but also was suitable for the efficient and simultaneous removal of multicomponent VOCs (toluene, benzene, acetone, and chlorobenzene). This work also provided an idea for the further development of high-efficiency catalysts for the purification of VOCs from complex atmosphere environment.
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We report a method for the electrochemical deuteration of α,ß-unsaturated carbonyl compounds under catalyst- and external-reductant-free conditions, with deuteration rates as high as 99 % and yields up to 91 % in 2â h. The use of graphite felt for both the cathode and the anode was key to ensuring chemoselectivity and high deuterium incorporation under neutral conditions without the need for an external reductant. This method has a number of advantages over previously reported deuteration reactions that use stoichiometric metallic reductants. Mechanistic experiments showed that O2 evolution at the anode not only eliminates the need for an external reductant but also regulates the pH of the reaction mixture, keeping it approximately neutral.
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In this Letter, we propose that the x-ray and the TeV observations in the vicinity of Geminga can be understood in the framework of anisotropic diffusion of injected electrons or positrons. This interpretation only requires the turbulence in the vicinity of Geminga to be sub-Alfvénic with the local mean magnetic field direction approximately aligned with our line of sight towards Geminga, without invoking extreme conditions for the environment, such as an extremely small diffusion coefficient and a weak magnetic field of submicrogauss as suggested in previous literature.
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The North Atlantic red alga Mastocarpus stellatus is characterized by two life histories (sexual-type and direct-type), which correspond to two geographically isolated breeding groups. These features enable M. stellatus to be an interesting model to investigate how environmental shift and apomictic propagation have influenced its population genetic structure, historical demography and distribution dynamic. To test these ideas, we obtained 456 specimens from 15 locations on both sides of the North Atlantic and sequenced portion of the nuclear internal transcribed spacer (ITS), mitochondrial cox2-3 region (COX) and plastid RuBisCo spacer (RLS). Median-joining networks and ML trees inferred from COX and RLS consistently revealed two gene lineages (mtDNA: CN, CS; cpDNA: RN, RS). The concatenated COX and RLS markers yielded three cytotypes: a northern CN-RN, a southern CS-RS and a mixed cytotype CS-RN, which enabled us to roughly separate samples into D (direct-type life-cycle) and S (sexual-type life-cycle) groups (northern CN-RN and mixed cytotype CS-RN=D; southern CS-RS=S). Pairwise FST analysis of the D group revealed a high level of genetic differentiation both along European coasts and across the Atlantic basin. Bayesian skyline plots (BSPs) and IMa analyses indicated that M. stellatus underwent slight demographic expansion at the late-Pleistocene, with the beginning of divergence between lineages dating to c. 0.189Ma (95%HPD: 0.083-0.385Ma). IMa analyses also revealed asymmetric genetic exchange among European populations and a predominant postglacial trans-Atlantic migration from Norway and Galway Bay to North America. Our study highlights the importance of phylogeographic approaches to discover the imprints of climate change, life histories and gene flow in driving population genetic connectivity and biogeographic distribution of intertidal seaweeds in the North Atlantic.
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Algas Marinas/genética , Secuencia de Bases , Teorema de Bayes , Cambio Climático , ADN de Cloroplastos/genética , ADN Mitocondrial/genética , Flujo Génico , Variación Genética , Genética de Población , América del Norte , Filogenia , Filogeografía , Rhodophyta/genética , Algas Marinas/clasificación , Análisis de Secuencia de ADNRESUMEN
It was recently proposed that a giant flare of the blazar PKS B1424-418 at redshift z=1.522 is in association with a PeV-energy neutrino event detected by IceCube. Based on this association we here suggest that the flight time difference between the PeV neutrino and gamma-ray photons from blazar flares can be used to constrain the violations of equivalence principle and the Lorentz invariance for neutrinos. From the calculated Shapiro delay due to clusters or superclusters in the nearby universe, we find that violation of the equivalence principle for neutrinos and photons is constrained to an accuracy of at least 10^{-5}, which is 2 orders of magnitude tighter than the constraint placed by MeV neutrinos from supernova 1987A. Lorentz invariance violation (LIV) arises in various quantum-gravity theories, which predicts an energy-dependent velocity of propagation in vacuum for particles. We find that the association of the PeV neutrino with the gamma-ray outburst set limits on the energy scale of possible LIV to >0.01E_{pl} for linear LIV models and >6×10^{-8}E_{pl} for quadratic order LIV models, where E_{pl} is the Planck energy scale. These are the most stringent constraints on neutrino LIV for subluminal neutrinos.
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BACKGROUND: Circular RNA (CircRNA) is known to play an important role in cardiovascular diseases, but its use as a biomarker of acute myocardial infarction (AMI) has not been studied. This study explores the feasibility of circPRDM5 as a novel biomarker of AMI. METHODS: CircPRDM5 was screened by bioinformatics, the correct circPRDM5 primers were tested by agarose gel electrophoresis (AGE) and Sanger sequencing, and the expression level of serum circPRDM5 was detected by Quantitative Reverse Transcription-Polymerase Chain Reaction. (qRT-PCR), and the diagnostic value of circPRDM5 was analyzed by the receiver operating characteristic (ROC) curve. RESULTS: The expression of circPRDM5 in serum of AMI patients was significantly decreased compared with that of healthy control group and angina group (P < 0.001). The area under ROC curve of serum circPRDM5 was 0.862 [95 % CI, 0.814-0.909]. The combined diagnosis of serum circPRDM5, cardiac troponin T (cTnT) and creatine kinase-MB (CK-MB) could improve the sensitivity of diagnosing AMI. The expression level of serum circPRDM5 increased after percutaneous coronary intervention (PCI). CONCLUSIONS: CircPRDM5 can be used as a novel biomarker for AMI, and its combination with cTnT and CK-MB can improve diagnostic value.
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Infarto del Miocardio , Intervención Coronaria Percutánea , Humanos , Infarto del Miocardio/diagnóstico , Infarto del Miocardio/genética , Troponina T/genética , Curva ROC , Forma MB de la Creatina-Quinasa , BiomarcadoresRESUMEN
As a photostabilizing agent for cyanine dye, methyl-ß-cyclodextrin (MßCD) was investigated as a possible antifading agent for cyanine dye-labeled proteins. Cyanine-3 (Cy3)-labeled streptavidin (SA-Cy3) solutions containing MßCD exhibited improved resistance against photobleaching. Further research revealed that MßCD can be used as a coating material on the surface of gene chips. Chips loaded with cyanine dye (Cy3 and Cyanine-5 (Cy5))-conjugated model microbeads exhibited resistance against photobleaching with MßCD coatings. MßCD coatings improved the imaging quality of model chips and resulted in higher discrimination ratios (DR) of single base recognition by a set of control beads (NP68). In a whole genome genotyping assay for human samples, the MßCD-coated samples were found to have a better clustering performance than the noncoated ones for a group of randomly picked single nucleotide polymorphisms (SNPs).
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BACKGROUND: Glioblastoma are highly malignant type of primary brain tumors. Treatment for glioblastoma multiforme (GBM) generally involves surgery combined with chemotherapy and radiotherapy. However, the development of tumoral chemo- and radioresistance induces complexities in clinical practice. Multiple signaling pathways are known to be involved in radiation-induced cell survival. However, the role of alpha-thalassemia X-linked mutant retardation syndrome (ATRX), a chromatin remodeling protein, in GBM radioresistance remains unclear. METHODS: In the present study, the ATRX mutation rate in patients with glioma was obtained from The Cancer Genome Atlas, while its expression analyzed using bioinformatics. Datasets were also obtained from the Gene Expression Omnibus, and ATRX expression levels following irradiation of GBM were determined. The effects of ATRX on radiosensitivity were investigated using a knockdown assays. RESULTS: The present study demonstrated that the ATRX mutation rate in patients with GBM was significantly lower than that in patients with low-grade glioma, and that patients harboring an ATRX mutation exhibited a prolonged survival, compared with to those harboring the wild-type gene. Single-cell RNA sequencing demonstrated that ATRX counts increased 2 days after irradiation, with ATRX expression levels also increasing in U-251MG radioresistant cells. Moreover, the results of in vitro irradiation assays revealed that ATRX expression was increased in U-251MG cells, while ATRX knockdown was associated with increased levels of radiosensitivity. CONCLUSIONS: High ATRX expression levels in primary GBM may contribute to high levels of radioresistance. Thus ATRX is a potential target for overcoming the radioresistance in GBM.