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BACKGROUND: Increasing evidence suggests that DXS253E is critical for cancer development and progression, but the function and potential mechanism of DXS253E in colorectal cancer (CRC) remain largely unknown. In this study, we evaluated the clinical significance and explored the underlying mechanism of DXS253E in CRC. METHODS: DXS253E expression in cancer tissues was investigated using the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The Kaplan-Meier plot was used to assess the prognosis of DXS253E. The cBioPortal, MethSurv, and Tumor Immune Estimation Resource (TIMER) databases were employed to analyze the mutation profile, methylation, and immune infiltration associated with DXS253E. The biological functions of DXS253E in CRC cells were determined by CCK-8 assay, plate cloning assay, Transwell assay, flow cytometry, lactate assay, western blot, and qRT-PCR. RESULTS: DXS253E was upregulated in CRC tissues and high DXS253E expression levels were correlated with poor survival in CRC patients. Our bioinformatics analyses showed that high DXS253E gene methylation levels were associated with the favorable prognosis of CRC patients. Furthermore, DXS253E levels were linked to the expression levels of several immunomodulatory genes and an abundance of immune cells. Mechanistically, the overexpression of DXS253E enhanced proliferation, migration, invasion, and the aerobic glycolysis of CRC cells through the AKT/mTOR pathway. CONCLUSIONS: We demonstrated that DXS253E functions as a potential role in CRC progression and may serve as an indicator of outcomes and a therapeutic target for regulating the AKT/mTOR pathway in CRC.
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BACKGROUND: Although recent studies provide mechanistic understanding to the pathogenesis of radiation induced lung injury (RILI), rare therapeutics show definitive promise for treating this disease. Type II alveolar epithelial cells (AECII) injury in various manner results in an inflammation response to initiate RILI. RESULTS: Here, we reported that radiation (IR) up-regulated the TNKS1BP1, causing progressive accumulation of the cellular senescence by up-regulating EEF2 in AECII and lung tissue of RILI mice. Senescent AECII induced Senescence-Associated Secretory Phenotype (SASP), consequently activating fibroblasts and macrophages to promote RILI development. In response to IR, elevated TNKS1BP1 interacted with and decreased CNOT4 to suppress EEF2 degradation. Ectopic expression of EEF2 accelerated AECII senescence. Using a model system of TNKS1BP1 knockout (KO) mice, we demonstrated that TNKS1BP1 KO prevents IR-induced lung tissue senescence and RILI. CONCLUSIONS: Notably, this study suggested that a regulatory mechanism of the TNKS1BP1/CNOT4/EEF2 axis in AECII senescence may be a potential strategy for RILI.
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Células Epiteliais Alveolares , Senescência Celular , Camundongos Endogâmicos C57BL , Camundongos Knockout , Animais , Camundongos , Senescência Celular/efeitos da radiação , Senescência Celular/fisiologia , Células Epiteliais Alveolares/metabolismo , Células Epiteliais Alveolares/efeitos da radiação , Células Epiteliais Alveolares/patologia , Lesão Pulmonar/metabolismo , Lesão Pulmonar/genética , Lesão Pulmonar/patologia , Quinase do Fator 2 de Elongação/metabolismo , Quinase do Fator 2 de Elongação/genética , Humanos , Lesões Experimentais por Radiação/metabolismo , Lesões Experimentais por Radiação/patologia , Lesões Experimentais por Radiação/genética , Células Cultivadas , MasculinoRESUMO
This paper investigates the problem of synthesizing network attacks against fault diagnosis in the context of discrete event systems (DESs). It is assumed that the sensor observations sent to the operator that monitors a system are tampered with by an active attacker. We first formulate the process of online fault diagnosis under attack. Then, from the attack viewpoint, we define a sensor network attacker as successful if it can degrade the fault diagnosis in the case of maintaining itself as undiscovered by the operator. To verify such an attacker, an information structure called a joint diagnoser (JD) is proposed, which describes all possible attacks in a given attack scenario. Based on the refined JD, i.e., stealthy joint diagnoser (SJD), we present an algorithmic procedure for synthesizing a successful attacker if it exists.
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OBJECTIVES: Darkening has been an issue of concern for foundation products. The secretion of sebum plays a significant role in the process of foundation darkening, but the underlying mechanisms and solutions have been rarely reported. The aim of this study was to explore the relationship between sebum secretion and liquid foundation darkening and to provide possible solutions for reducing sebum-induced darkening in liquid foundation. METHODS: Artificial sebum in different concentrations was added to a basic liquid foundation to simulate different stages of sebum secretion. The colour of the mixture was then measured by a spectrophotometer on the standard opacity chart. Potential technical solutions for anti-darkening were applied to a basic liquid foundation, and its ability to anti-darkening was further verified in vivo. RESULTS: (1) The influences of sebum addition on liquid foundation darkening had a significant positive correlation with the increase in transmissivities (R2 = 0.852, p < 0.01). (2) A certain range of sebum addition can reduce the darkening of volatile foundations. (3) The liquid foundations using pigments with high dispersibility in sebum were less influenced by sebum. (4) The replacement of pigments with oil-fixing ability could effectively reduce the darkening of liquid foundations induced by sebum (p < 0.01). CONCLUSION: The effect of sebum on the darkening of liquid foundation was accompanied by a greater transmissivity as its pigment concentration decreased. Balanced volatility, the addition of powders with higher sebum dispersibility and the replacement of oil-fixing powders could reduce the darkening of the liquid foundation caused by sebum secretion.
OBJECTIFS: L'assombrissement a été un problème de préoccupation pour les produits de fond de teint. La sécrétion de sébum joue un rôle significatif dans le processus d'assombrissement du fond de teint, mais les mécanismes sous-jacents et les solutions ont été rarement rapportés. L'objectif de cette étude était d'explorer la relation entre la sécrétion de sébum et l'assombrissement du fond de teint liquide, et de fournir des solutions possibles pour réduire l'assombrissement induit par le sébum dans le fond de teint liquide. MÉTHODES: Du sébum artificiel à différentes concentrations a été ajouté à un fond de teint liquide de base pour simuler différents stades de sécrétion de sébum. La couleur du mélange a ensuite été mesurée par un spectrophotomètre sur le tableau standard d'opacité. Des solutions techniques potentielles pour l'anti-assombrissement ont été appliquées à un fond de teint liquide de base et leur capacité à prévenir l'assombrissement a été vérifiée in vivo. RÉSULTATS: (1) Les influences de l'ajout de sébum sur l'assombrissement du fond de teint liquide avaient une corrélation significativement positive avec l'augmentation des transmissivités (R2 = 0.852 p < 0.01). (2) Une certaine plage de concentration de sebum peut réduire l'assombrissement des fondations volatiles. (3) Les fonds de teint liquides utilisant des pigments à haute dispersibilité dans le sébum étaient moins influencés par le sébum. (4) Le remplacement des pigments par des poudres à capacité de fixation d'huile pouvait efficacement réduire l'assombrissement des fonds de teint liquides induit par le sébum (p < 0.01). CONCLUSION: L'effet du sébum sur l'assombrissement du fond de teint liquide était accompagné d'une plus grande transmissivité à mesure que la concentration de son pigment diminuait. La volatilité équilibrée, l'ajout de poudres à plus grande dispersibilité de sébum et le remplacement de poudres à capacité de fixation d'huile pourraient réduire l'assombrissement du fond de teint liquide causé par la sécrétion de sébum.
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Sebo , Fenômenos Fisiológicos da Pele , EspectrofotometriaRESUMO
Molecular dynamics (MD) is a widely-used tool for simulating molecular and materials properties. It is common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that molecular dynamics simulations are energy conserving. The emergence of machine learning (ML) potentials for MD leads to a growing realization that monitoring conservation of energy during simulations is of low utility because the dynamics is often unphysically dissociative. Other ML methods for MD are not based on a potential and provide only forces or trajectories which are reasonable but not necessarily energy-conserving. Here we propose to clearly distinguish between the simulation-energy and true-energy conservation and highlight that the simulations should focus on decreasing the degree of true-energy non-conservation. We introduce very simple, new criteria for evaluating the quality of molecular dynamics by estimating the degree of true-energy non-conservation and we demonstrate their practical utility on an example of infrared spectra simulations. These criteria are more important and intuitive than simply evaluating the quality of the ML potential energies and forces as is commonly done and can be applied universally, e.g., even for trajectories with unknown or discontinuous potential energy. Such an approach introduces new standards for evaluating MD by focusing on the true-energy conservation and can help in developing more accurate methods for simulating molecular and materials properties.
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This study investigated the effect of the landscape pattern of permeable/impermeable patches on NO3--N and particulate organic nitrogen (PON) concentrations during stormwater runoff transport and their source contributions. Six landscape pattern indices, namely, mean proximity index (MPI), largest patch index (LPI), mean shape index (MSI), landscape shape index (LSI), connect index (CONNECT), and splitting index (SPLIT), were selected to reflect the fragmentation, complexity, and connectivity of permeable patches in urban catchments. The results show that lower fragmentation, higher complexity, and greater connectivity can reduce NO3--N concentrations in road runoff and drainage flow (i.e., the flow in the stormwater drainage network), as well as PON concentrations in road runoff. Further, the above landscape pattern is effective for mitigating the contributions of NO3--N and PON from road runoff. Low impact development (LID) can be incorporated with the landscape pattern of permeable/impermeable patches to mitigate nitrogen pollution in urban stormwater at the catchment scale by optimizing the spatial arrangement.
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Nitratos , Poluentes Químicos da Água , Nitratos/análise , Nitrogênio/análise , Monitoramento Ambiental/métodos , Movimentos da Água , Poluentes Químicos da Água/análise , Chuva , Compostos Orgânicos/análise , PoeiraRESUMO
A multi-channel surface electromyography wireless acquisition system is designed, which is mainly composed of ADS1299 integrated analog front-end chip and CC3200 wireless MCU of TI company. The key indicators of hardware are measured according to the industry standard, and the results are better than the industry standard, which can meet the continuous use of multi-scene tasks. This system has the advantages of high performance, low power consumption and small size. It has been applied to the detection of surface EMG signal in motion gesture recognition and has a good application value.
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Gestos , Processamento de Sinais Assistido por Computador , Eletromiografia , Movimento (Física) , Tecnologia sem FioRESUMO
OBJECTIVES: Breast cancer is a popular fatal malignant tumor for women with high of rates incidence and mortality. Development of the new approaches for breast cancer targeted diagnosis and chemotherapy is emergently needed by the current clinical practice, the important first step is finding a breast cancer specifically binding molecule or fragment as early clinical indicators. RESULTS: By a phage-displayed peptide library, a 12-mer peptide, CSB1 was screened out using MCF-7 cells as the target. The consequently results under immunofluorescence and laser scanning confocal microscope (LSCM) indicated that CSB1 bound MCF-7 cells and breast cancer tissues specifically and sensitively with high affinity. Bioinformatics analysis suggested that the peptide CSB1 targets the 5-Lipoxygenase-Activating Protein (FLAP), which has been implicated in breast cancer progression and prognosis. CONCLUSIONS: The peptide, CSB1 is of the potential as a candidate to be used for developing the new approaches of molecular imaging detection and targeting chemotherapy of breast cancer in the future.
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Bioprospecção/métodos , Neoplasias da Mama , Biblioteca de Peptídeos , Peptídeos , Mama/química , Mama/metabolismo , Neoplasias da Mama/química , Neoplasias da Mama/metabolismo , Linhagem Celular Tumoral , Feminino , Humanos , Células MCF-7 , Peptídeos/análise , Peptídeos/química , Peptídeos/metabolismoRESUMO
A Gram-stain-positive, non-motile, creamy-white actinobacterium, which has an elementary branching rod-coccus life cycle was isolated from the rhizosphere soil of rice (Oryza sativa L.) collected from Northeast Agricultural University in Harbin, Heilongjiang province, north-east PR China, and its taxonomic status was examined by using a polyphasic approach. Results from the 16S rRNA gene sequence study showed that the isolate, designated strain NEAU-CX67T, belonged to the genus Rhodococcus and formed a cluster with Rhodococcus maanshanensis DSM 44675T, Rhodococcus kronopolitis NEAU-ML12T and Rhodococcus tukisamuensis JCM 11308T (98.3, 98.1 and 97.7% gene sequence similarity, respectively). The major fatty acids were C16â:â0, 10-methyl C18â:â0, C18â:â1 ω9c and C16â:â1 ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major isoprenoid quinone was MK-8(H2). Whole-cell hydrolysates contained meso-diaminopimelic acid. Arabinose, galactose and ribose were detected as diagnostic sugars from whole-cell hydrolysates. Mycolic acids were detected. The genomic DNA G+C content of strain NEAU-CX67T was 64.6 mol%. Strain NEAU-CX67T exhibited low average nucleotide identity and digital DNA-DNA hybridization values with R. maanshanensis DSM 44675T (92.1 and 45.4â%) and R. tukisamuensis JCM 11308T (81.9 and 24.4â%). On the basis of results of phylogenetic, genotypic, physiological and chemotaxonomic analysis, strain NEAU-CX67T is considered to represent a novel species of the genus Rhodococcus for which the name Rhodococcus oryzae sp. nov. is proposed. The type strain is NEAU-CX67T (=DSM 107701T=CCTCC AB 2018233T).
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Oryza/microbiologia , Filogenia , Rizosfera , Rhodococcus/classificação , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Rhodococcus/isolamento & purificação , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/químicaRESUMO
'Targeting peptides' have demonstrated their value in diagnostic imaging and therapy and novel peptide probes specific to cervical cancer were developed. In the M13KE phage dodecapeptide (12-mer) peptide library, the phage clone S7 showed the best binding to the cancer cells as confirmed by immunofluorescence and flow cytometry assays, and was selected for continued studies. Its binding peptide, CSP3, was synthesized from the sequence of S7's 12-mer at the N-terminus of the minor coat protein pIII of this M13KE phage vector. The peptide's binding was analyzed by the same assays used for S7. It was also assessed using competitive inhibition and binding to a tissue chip. The results demonstrated that the CSP3 peptide bound to cervical carcinoma cells with high sensitivity and specificity. The positive results indicated that the peptide CSP3, conjugated with nanomaterials and chemotherapeutics, may be developed as a targeting vehicle for therapeutic drug delivery against cervical cancer, especially cervical cancer with multiple drug resistance. For this aim, we prepared a CSP3 conjugated liposome drug delivery system containing doxorubicin (DOX) and microRNA101 (miR101) expression plasmids (CSP3-Lipo-DOX-miR101), and the primary result showed that the system demonstrated significantly enhanced cytotoxicity to SiHa cells and DOX resistant SiHa cells, SiHa/ADR. Our results showed that CSP3 is a cervical cancer targeting 12aa peptide with high specificity and sensitivity, and the CSP3 conjugated drug delivery system, CSP3-Lipo-DOX-miR101 has promising potential for development as an efficient drug system for the therapy of cervical cancer.
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Doxorrubicina/análogos & derivados , MicroRNAs/farmacologia , Peptídeos/metabolismo , Neoplasias do Colo do Útero/metabolismo , Adulto , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Doxorrubicina/química , Doxorrubicina/farmacologia , Sistemas de Liberação de Medicamentos , Feminino , Humanos , MicroRNAs/química , Pessoa de Meia-Idade , Biblioteca de Peptídeos , Peptídeos/química , Peptídeos/isolamento & purificação , Polietilenoglicóis/química , Polietilenoglicóis/farmacologia , Neoplasias do Colo do Útero/terapiaRESUMO
Annexin A2 (ANXA2) is reported to be associated with cancer development. To investigate the roles ANXA2 plays during the development of cancer, the RNAi method was used to inhibit the ANXA2 expression in caco2 (human colorectal cancer cell line) and SMMC7721 (human hepatocarcinoma cell line) cells. The results showed that when the expression of ANXA2 was efficiently inhibited, the growth and motility of both cell lines were significantly decreased, and the development of the motility relevant microstructures, such as pseudopodia, filopodia, and the polymerization of microfilaments and microtubules were obviously inhibited. The cancer cell apoptosis was enhanced without obvious significance. The possible regulating pathway in the process was also predicted and discussed. Our results suggested that ANXA2 plays important roles in maintaining the malignancy of colorectal and hepatic cancer by enhancing the cell proliferation, motility, and development of the motility associated microstructures of cancer cells based on a possible complicated signal pathway.
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Anexina A2/metabolismo , Carcinogênese , Carcinoma Hepatocelular/fisiopatologia , Neoplasias Colorretais/fisiopatologia , Citoesqueleto/metabolismo , Neoplasias Hepáticas/fisiopatologia , Anexina A2/genética , Linhagem Celular Tumoral , Movimento Celular , Proliferação de Células , Inativação Gênica , Humanos , Modelos Biológicos , Interferência de RNARESUMO
This study was to investigate the changes of microbial community and counts of MAP pot-stewed duck wing (PSDW) under different packaging films and spices ratio during 15 °C storage, using the traditional bacterial cultivation and PCR-DGGE. Results of microbial counting showed that the shelf-life of PDSW during 15 °C storage for recommendation was within six days, and the packaging films and spices ratio didn't affect the change of microbial numbers in PSDW during storage. PCR-DGGE analysis revealed that Staphylococcus equorum, Weissella sp., Leuconostoc mesenteroides became the dominating bacteria of PSDW at the end of storage, and high barrier cover film, general barrier base film and spice ratio 1:1, had a better inhibition effect on bacteria in PSDW products, which could be used as the condition for PSDW storage. This study will help PSDW processing enterprises visualize the biodiversity of PSDW during storage, and choose the best condition for the subsequent processing.
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As a generalized quantum machine learning model, parameterized quantum circuits (PQC) have been found to perform poorly in terms of classification accuracy and model scalability for multi-category classification tasks. To address this issue, we propose a scalable parameterized quantum circuits classifier (SPQCC), which performs per-channel PQC and combines the measurements as the output of the trainable parameters of the classifier. By minimizing the cross-entropy loss through optimizing the trainable parameters of PQC, SPQCC leads to a fast convergence of the classifier. The parallel execution of identical PQCs on different quantum machines with the same structure and scale reduces the complexity of classifier design. Classification simulations performed on the MNIST Dataset show that the accuracy of our proposed classifier far exceeds that of other quantum classification algorithms, achieving the state-of-the-art simulation result and surpassing/reaching classical classifiers with a considerable number of trainable parameters. Our classifier demonstrates excellent scalability and classification performance.
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Existing robotic systems have a tension between generality and precision. Deployed solutions for robotic manipulation tend to fall into the paradigm of one robot solving a single task, lacking "precise generalization," or the ability to solve many tasks without compromising on precision. This paper explores solutions for precise and general pick and place. In precise pick and place, or kitting, the robot transforms an unstructured arrangement of objects into an organized arrangement, which can facilitate further manipulation. We propose SimPLE (Simulation to Pick Localize and placE) as a solution to precise pick and place. SimPLE learns to pick, regrasp, and place objects given the object's computer-aided design model and no prior experience. We developed three main components: task-aware grasping, visuotactile perception, and regrasp planning. Task-aware grasping computes affordances of grasps that are stable, observable, and favorable to placing. The visuotactile perception model relies on matching real observations against a set of simulated ones through supervised learning to estimate a distribution of likely object poses. Last, we computed a multistep pick-and-place plan by solving a shortest-path problem on a graph of hand-to-hand regrasps. On a dual-arm robot equipped with visuotactile sensing, SimPLE demonstrated pick and place of 15 diverse objects. The objects spanned a wide range of shapes, and SimPLE achieved successful placements into structured arrangements with 1-mm clearance more than 90% of the time for six objects and more than 80% of the time for 11 objects.
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Wnt signaling pathways are highly conserved cascades that mediate multiple biological processes through canonical or noncanonical pathways, from embryonic development to tissue maintenance, but they also contribute to the pathogenesis of numerous cancers. Recent studies have revealed that Wnt signaling pathways critically control the interplay between cancer cells and tumor-associated macrophages (TAMs) in the tumor microenvironment (TME) and potentially impact the efficacy of cancer immunotherapy. In this review, we summarize the evidence that Wnt signaling pathways boost the maturation and infiltration of macrophages for immune surveillance in the steady state but also polarize TAMs toward immunosuppressive M2-like phenotypes for immune escape in the TME. Both cancer cells and TAMs utilize Wnt signaling to transmit signals, and this interaction is crucial for the carcinogenesis and progression of common solid cancers, such as colorectal, gastric, hepatocellular, breast, thyroid, prostate, kidney, and lung cancers; osteosarcoma; and glioma. Specifically, compared with those in solid cancers, Wnt signaling pathways play a distinct role in the pathogenesis of leukemia. Efforts to develop Wnt-based drugs for cancer treatment are still ongoing, and some indeed enhance the anticancer immune response. We believe that the combination of Wnt signaling-based therapy with conventional or immune therapies is a promising therapeutic approach and can facilitate personalized treatment for most cancers.
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Neoplasias , Via de Sinalização Wnt , Masculino , Humanos , Macrófagos Associados a Tumor , Neoplasias/tratamento farmacológico , Macrófagos/metabolismo , Imunoterapia , Microambiente TumoralRESUMO
The rapid advancement in the fabrication and culture of in vitro organs has marked a new era in biomedical research. While strides have been made in creating structurally diverse bioartificial organs, such as the liver, which serves as the focal organ in our study, the field lacks a uniform approach for the predictive assessment of liver function. Our research bridges this gap with the introduction of a novel, machine-learning-based "3P model" framework. This model draws on a decade of experimental data across diverse culture platform studies, aiming to identify critical fabrication parameters affecting liver function, particularly in terms of albumin and urea secretion. Through meticulous statistical analysis, we evaluated the functional sustainability of the in vitro liver models. Despite the diversity of research methodologies and the consequent scarcity of standardized data, our regression model effectively captures the patterns observed in experimental findings. The insights gleaned from our study shed light on optimizing culture conditions and advance the evaluation of the functional maintenance capacity of bioartificial livers. This sets a precedent for future functional evaluations of bioartificial organs using machine learning.
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Órgãos Bioartificiais , Fígado Artificial , Fígado , AlbuminasRESUMO
We present an open-source MLatom@XACS software ecosystem for on-the-fly surface hopping nonadiabatic dynamics based on the Landau-Zener-Belyaev-Lebedev algorithm. The dynamics can be performed via Python API with a wide range of quantum mechanical (QM) and machine learning (ML) methods, including ab initio QM (CASSCF and ADC(2)), semiempirical QM methods (e.g., AM1, PM3, OMx, and ODMx), and many types of ML potentials (e.g., KREG, ANI, and MACE). Combinations of QM and ML methods can also be used. While the user can build their own combinations, we provide AIQM1, which is based on Δ-learning and can be used out-of-the-box. We showcase how AIQM1 reproduces the isomerization quantum yield of trans-azobenzene at a low cost. We provide example scripts that, in dozens of lines, enable the user to obtain the final population plots by simply providing the initial geometry of a molecule. Thus, those scripts perform geometry optimization, normal mode calculations, initial condition sampling, parallel trajectories propagation, population analysis, and final result plotting. Given the capabilities of MLatom to be used for training different ML models, this ecosystem can be seamlessly integrated into the protocols building ML models for nonadiabatic dynamics. In the future, a deeper and more efficient integration of MLatom with Newton-X will enable a vast range of functionalities for surface hopping dynamics, such as fewest-switches surface hopping, to facilitate similar workflows via the Python API.
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Thyroid cancer incidence increases worldwide annually, primarily due to factors such as ionizing radiation (IR), iodine intake, and genetics. Papillary carcinoma of the thyroid (PTC) accounts for about 80% of thyroid cancer cases. RET/PTC1 (coiled-coil domain containing 6 [CCDC6]-rearranged during transfection) rearrangement is a distinctive feature in over 70% of thyroid cancers who exposed to low doses of IR in Chernobyl and HiroshimaâNagasaki atomic bombings. This study aims to elucidate mechanism between RET/PTC1 rearrangement and IR in PTC. N-thy-ori-3-1 cells were subjected to varying doses of IR (2/1/0.5/0.2/0.1/0.05 Gy) of IR at different days, and result showed low-dose IR-induced RET/PTC1 rearrangement in a dose-dependent manner. RET/PTC1 has been observed to promote PTC both in vivo and in vitro. To delineate the role of different DNA repair pathways, SCR7, RI-1, and Olaparib were employed to inhibit non-homologous end joining (NHEJ), homologous recombination (HR), and microhomology-mediated end joining (MMEJ), respectively. Notably, inhibiting NHEJ enhanced HR repair efficiency and reduced IR-induced RET/PTC1 rearrangement. Conversely, inhibiting HR increased NHEJ repair efficiency and subsequent RET/PTC1 rearrangement. The MMEJ did not show a markable role in this progress. Additionally, inhibiting DNA-dependent protein kinase catalytic subunit (DNA-PKcs) decreased the efficiency of NHEJ and thus reduced IR-induced RET/PTC1 rearrangement. To conclude, the data suggest that NHEJ, rather than HR or MMEJ, is the critical cause of IR-induced RET/PTC1 rearrangement. Targeting DNA-PKcs to inhibit the NHEJ has emerged as a promising therapeutic strategy for addressing IR-induced RET/PTC1 rearrangement in PTC.
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Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program package designed to leverage the power of ML to enhance typical computational chemistry simulations and to create complex workflows. This open-source package provides plenty of choice to the users who can run simulations with the command-line options, input files, or with scripts using MLatom as a Python package, both on their computers and on the online XACS cloud computing service at XACScloud.com. Computational chemists can calculate energies and thermochemical properties, optimize geometries, run molecular and quantum dynamics, and simulate (ro)vibrational, one-photon UV/vis absorption, and two-photon absorption spectra with ML, quantum mechanical, and combined models. The users can choose from an extensive library of methods containing pretrained ML models and quantum mechanical approximations such as AIQM1 approaching coupled-cluster accuracy. The developers can build their own models using various ML algorithms. The great flexibility of MLatom is largely due to the extensive use of the interfaces to many state-of-the-art software packages and libraries.
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INTRODUCTION: Radiation-induced pulmonary fibrosis (RIPF) is a chronic, progressive, irreversible lung interstitial disease that develops after radiotherapy. Although several previous studies have focused on the mechanism of epithelial-mesenchymal transition (EMT) in lung epithelial cells, the essential factors involved in this process remain poorly understood. The DNA-dependent protein kinase catalytic subunit (DNA-PKcs) exhibits strong repair capacity when cells undergo radiation-induced damage; whether DNA-PKcs regulates EMT during RIPF remains unclear. OBJECTIVES: To investigate the role and molecular mechanism of DNA-PKcs in RIPF and provide an important theoretical basis for utilising DNA-PKcs-targeted drugs for preventing RIPF. METHODS: DNA-PKcs knockout (DPK-/-) mice were generated via the Cas9/sgRNA technique and subjected to whole chest ionizing radiation (IR) at a 20 Gy dose. Before whole chest IR, the mice were intragastrically administered the DNA-PKcs-targeted drug VND3207. Lung tissues were collected at 1 and 5 months after IR. RESULTS: The expression of DNA-PKcs is low in pulmonary fibrosis (PF) patients. DNA-PKcs deficiency significantly exacerbated RIPF by promoting EMT in lung epithelial cells. Mechanistically, DNA-PKcs deletion by shRNA or inhibitor NU7441 maintained the protein stability of Twist1. Furthermore, AKT1 mediated the interaction between DNA-PKcs and Twist1. High Twist1 expression and EMT-associated changes caused by DNA-PKcs deletion were blocked by insulin-like growth factor-1 (IGF-1), an AKT1 agonist. The radioprotective drug VND3207 prevented IR-induced EMT and alleviated RIPF in mice by stimulating the kinase activity of DNA-PKcs. CONCLUSION: Our study clarified the critical role and mechanism of DNA-PKcs in RIPF and showed that it could be a potential target for preventing RIPF.