Instrumentation and development of a mass spectrometry system for the study of gas-phase biomolecular ion reactions

Gas-phase reactions of biomolecular ions are highly relevant to the understanding of structures and functions of the biomolecules. Mass spectrometry is a powerful tool in investigating gas-phase ion chemistry. Various mass spectrometers have been developed to explore ion/molecule reactions, ion/ion reactions, ion/photon reactions, ion/radical reactions etc., both at atmospheric pressure and in vacuum. In-vacuum reactions have an advantage of involving pre-selecting the ions for the reactions using a mass analyzer. Over the decades, a variety of mass analyzers have been employed in the research of ion chemistry. Hybrid configurations, such as quadrupole ion trap with a time-of-flight and or a quadrupole ion trap tandem with an Orbitrap, have been utilized to improve the performances for both the reaction (in trapping mode) and the mass analysis (accurate mass measurements). Complicated instrument structures, including ion optics, multiple mass analyzers and differential pumping for high vacuum, are typically required for the mass spectrometers for gas phase ion chemistry study. An alternative approach is to simplify the instrumentation by using pulsed discontinuous atmospheric pressure interfaces for introducing ionic or neutral reactants and a single ion trap as both the reactor and the mass analyzer. Such a simple mass spectrometry system was set up and demonstrated using two discontinuous atmospheric pressure interfaces in the study for this thesis. It was capable of carrying out ion/molecule and ion/ion reactions at an elevated pressure without the needs of ion optics or differential pumping system. Together with a pyrolysis radical source, in-vacuum ion/radical reactions were performed and their associated chemistry was studied. Radicals are important intermediates related to biochemical processes and biological functions. There are very limited techniques to monitor the reactive intermediates in-situ during a multi-step reaction in aqueous phase. On the other hand, these intermediates can be cooled down and preserved into a single-step procedure in gas-phase reactions since they only occur via collisions. Therefore, the fundamental study of gas-phase radical ion chemistry will provide evidences of the reactivity, energetics, and structural information of biological radicals, which has the potential to solve puzzles of aging, disease biomarker identification, and enzymatic activities. Using the system described above, a new reaction between protonated alkyl amines and pyrolysis formed cyclopropenylidene carbene was discovered, as the first experimental evidence of the reactivity of cyclopropenylidene. Given the important role of cyclopropenylidene in the combustion chemistry, organic synthesis, and interstellar chemistry, it is highly desirable to establish a fundamental understanding of their physical and chemical properties. The amine/cyclopropenylidene reactions were systematically studied using both theoretical calculation and experimental evidences. A proton-bound dimer reaction mechanism was proposed, with the amine and the carbene sharing a proton to form a complex as the first step, which was closely related to the high gas-phase basicity of cyclopropenylidene. Subsequent unimolecular dissociation of the complex yielded three possible reaction pathways, including proton-transfer to the carbene, covalent product formation, and direct separation. These reactions were studied with a variety of alkyl amines of different gas-phase basicities. For the covalent complex formation, partial protonation on cyclopropenylidene within the dimer facilitates subsequent nucleophilic attack to the carbene carbon by the amine nitrogen and leads to a C-N bond formation. The highest yield of covalent complex was achieved with the gas-phase basicity of the amine slightly lower but comparable to cyclopropenylidene. The results demonstrated a new reaction pathway of cyclopropenylidene besides the formation of cyclopropenium, which has long been considered as a dead end in interstellar carbon chemistry. Further reactivity study of cyclopropenylidene towards biomolecular ions was also carried out for nucleobases, nucleosides, amino acids, peptides, proteins, and lipids. The reaction to form proton-bound dimer for protonated biomolecular ions remained as the dominant reaction pathway. Interestingly, other possible reaction pathways, such as modifications of thiyl group or disulfide bonds, double bond addition, and single bond insertion, were inhibited in gas-phase ion/carbene reactions. Such results inferred that the reactivity of neutral species was not directly applicable to ion reactions, with the proton involved in the gas-phase biomolecular ion reactions

PCR法による法医実務試料からの性別およびABO式血液型判定

取得学位 : 博士（医学）, 学位授与番号 : 医博甲第1191号, 学位授与年月日：平成8年3月25日,学位授与年：199

Development and validation of prognostic index based on purine metabolism genes in patients with bladder cancer

BackgroundBladder cancer (BLCA) is a prevalent malignancy affecting the urinary system and is associated with significant morbidity and mortality worldwide. Dysregulation of tumor metabolic pathways is closely linked to the initiation and proliferation of BLCA. Tumor cells exhibit distinct metabolic activities compared to normal cells, and the purine metabolism pathway, responsible for providing essential components for DNA and RNA synthesis, is believed to play a crucial role. However, the precise involvement of Purine Metabolism Genes (PMGs) in the defense mechanism against BLCA remains elusive.MethodsThe integration of BLCA samples from the TCGA and GEO datasets facilitated the quantitative evaluation of PMGs, offering potential insights into their predictive capabilities. Leveraging the wealth of information encompassing mRNAsi, gene mutations, CNV, TMB, and clinical features within these datasets further enriched the analysis, augmenting its robustness and reliability. Through the utilization of Lasso regression, a prediction model was developed, enabling accurate prognostic assessments within the context of BLCA. Additionally, co-expression analysis shed light on the complex relationship between gene expression patterns and PMGs, unraveling their functional relevance and potential implications in BLCA.ResultsPMGs exhibited increased expression levels in the high-risk cohort of BLCA patients, even in the absence of other clinical indicators, suggesting their potential as prognostic markers. GSEA revealed enrichment of immunological and tumor-related pathways specifically in the high-risk group. Furthermore, notable differences were observed in immune function and m6a gene expression between the low- and high-risk groups. Several genes, including CLDN6, CES1, SOST, SPRR2A, MYBPH, CGB5, and KRT1, were found to potentially participate in the oncogenic processes underlying BLCA. Additionally, CRTAC1 was identified as potential tumor suppressor genes. Significant discrepancies in immunological function and m6a gene expression were observed between the two risk groups, further highlighting the distinct molecular characteristics associated with different prognostic outcomes. Notably, strong correlations were observed among the prognostic model, CNVs, SNPs, and drug sensitivity profiles.ConclusionPMGs have been implicated in the etiology and progression of bladder cancer (BLCA). Prognostic models corresponding to this malignancy aid in the accurate prediction of patient outcomes. Notably, exploring the potential therapeutic targets within the tumor microenvironment (TME) such as PMGs and immune cell infiltration holds promise for effective BLCA management, albeit necessitating further research. Moreover, the identification of a gene signature associated with purine Metabolism presents a credible and alternative approach for predicting BLCA, signifying a burgeoning avenue for targeted therapeutic investigations in the field of BLCA

RingMo-lite: A Remote Sensing Multi-task Lightweight Network with CNN-Transformer Hybrid Framework

In recent years, remote sensing (RS) vision foundation models such as RingMo have emerged and achieved excellent performance in various downstream tasks. However, the high demand for computing resources limits the application of these models on edge devices. It is necessary to design a more lightweight foundation model to support on-orbit RS image interpretation. Existing methods face challenges in achieving lightweight solutions while retaining generalization in RS image interpretation. This is due to the complex high and low-frequency spectral components in RS images, which make traditional single CNN or Vision Transformer methods unsuitable for the task. Therefore, this paper proposes RingMo-lite, an RS multi-task lightweight network with a CNN-Transformer hybrid framework, which effectively exploits the frequency-domain properties of RS to optimize the interpretation process. It is combined by the Transformer module as a low-pass filter to extract global features of RS images through a dual-branch structure, and the CNN module as a stacked high-pass filter to extract fine-grained details effectively. Furthermore, in the pretraining stage, the designed frequency-domain masked image modeling (FD-MIM) combines each image patch's high-frequency and low-frequency characteristics, effectively capturing the latent feature representation in RS data. As shown in Fig. 1, compared with RingMo, the proposed RingMo-lite reduces the parameters over 60% in various RS image interpretation tasks, the average accuracy drops by less than 2% in most of the scenes and achieves SOTA performance compared to models of the similar size. In addition, our work will be integrated into the MindSpore computing platform in the near future

Tenascin-C predicts IVIG non-responsiveness and coronary artery lesions in kawasaki disease in a Chinese cohort

ObjectivesTo assess the predictive value of tenascin-C (TN-C) for intravenous immunoglobulin (IVIG) non-responsiveness and coronary artery lesions (CALs) development at the acute stage of Kawasaki disease, and to build novel scoring systems for identifying IVIG non-responsiveness and CALs.MethodsA total of 261 patients in acute-stage Kawasaki disease were included. Serum samples before IVIG initiation were collected and TN-C expression levels were measured using an enzyme-linked immunosorbent assay. In addition to TN-C, another fifteen clinical and laboratory parameters collected before treatment were compared between IVIG responsive and non-responsive groups, and between groups with and without CALs. Multiple logistic regression analyses were performed to construct new scoring systems for the prediction of IVIG non-responsiveness and CALs development.ResultsIVIG non-responsive group (n = 51) had significantly higher TN-C level compared to IVIG responsive group (n = 210) (15.44 vs. 12.38 IU/L, P < 0.001). A novel scoring system composed of TN-C, total bilirubin, serum sodium and albumin was established to predict IVIG non-responsiveness. Patients with a total score ≥ 2 points were classified as high-risk cases. With the sensitivity of 78.4% and specificity of 73.8%, the efficiency of our scoring system for predicting IVIG non-responsiveness was comparable to the Kobayashi system. Consistently, the group developing CALs at the acute stage (n = 42) had significantly higher TN-C level compared to the group without CALs (n = 219) (19.76 vs. 12.10 IU/L, P < 0.001). A new scoring system showed that patients with elevated TN-C, platelet count ≥ 450 × 109/L, and delayed initial infusion of IVIG had a higher risk of developing CALs. Individuals with a total score ≥ 3 points were classified as high-risk cases. The sensitivity and specificity of the novel simple system for predicting CALs development were 83.3% and 74.0%, respectively, yielding a better efficiency than the Harada score.ConclusionElevated TN-C appeared to be an independent risk factor for both IVIG non-responsiveness and CALs in Chinese children with KD. Our scoring systems containing TN-C is simple and efficient in the early identification of high-risk KD cases that could benefit from more individualized medications

De-escalated radiotherapy for HER2-overexpressing breast cancer patients with 1-3 positive lymph nodes undergoing anti-HER2 targeted therapy

BackgroundIn the era of anti-HER2 targeted therapy, the potential clinical feasibility of considering HER2-overexpressing breast cancer cases presenting with 1-3 positive axillary lymph nodes as low-risk, and thereby contemplating postoperative radiotherapy reduction, remains an important subject for in-depth examination. The aim of this retrospective study was to evaluate the effectiveness of de-escalated radiotherapy in T1-2N1M0 HER2-overexpressing breast cancer patients receiving anti-HER2 targeted therapy. Specifically, omitting regional lymph node irradiation (RNI) after breast-conserving surgery and only performing whole-breast irradiation or omitting postmastectomy radiation therapy.MethodsA retrospective analysis was conducted on 429 patients with stage T1-2N1M0 primary invasive HER2-overexpressing breast cancer from our center between 2004 and 2018. Patients who received anti-HER2 targeted therapy were divided into an RNI group and a no RNI group to assess the role of RNI. The prognostic role of RNI was investigated via the Kaplan-Meier method and Cox proportional hazards modeling.ResultsThe median follow-up time was 46.8 months (range 7.1–225.8 months). In the anti-HER2 targeted therapy group RNI yielded no significant improvements in invasive disease-free survival (IDFS) (p = 0.940), local-regional recurrence-free survival (p = 0.380), distant metastases-free survival (p = 0.698), or overall survival (p = 0.403). Estrogen receptor (ER) status (hazard ratio [HR] 0.105, 95% confidence interval [CI] 0.023–0.749, p = 0.004) and lymph vascular invasion status (LVI) (HR 5.721, 95% CI 1.586–20.633, p = 0.008) were identified as independent prognostic factors for IDFS, and ER-positive and LVI-negative patients exhibited better prognoses.ConclusionOmitting RNI may be a safe option in T1-2N1 HER2-overexpressing breast cancer patients receiving standardized anti-HER2 targeted therapy; particularly in ER-positive or LVI-negative subgroups

Antibacterial, injectable, and adhesive hydrogel promotes skin healing

With the development of material science, hydrogels with antibacterial and wound healing properties are becoming common. However, injectable hydrogels with simple synthetic methods, low cost, inherent antibacterial properties, and inherent promoting fibroblast growth are rare. In this paper, a novel injectable hydrogel wound dressing based on carboxymethyl chitosan (CMCS) and polyethylenimine (PEI) was discovered and constructed. Since CMCS is rich in -OH and -COOH and PEI is rich in -NH2, the two can interact through strong hydrogen bonds, and it is theoretically feasible to form a gel. By changing their ratio, a series of hydrogels can be obtained by stirring and mixing with 5 wt% CMCS aqueous solution and 5 wt% PEI aqueous solution at volume ratios of 7:3, 5:5, and 3:7. Characterized by morphology, swelling rate, adhesion, rheological properties, antibacterial properties, in vitro biocompatibility, and in vivo animal experiments, the hydrogel has good injectability, biocompatibility, antibacterial (Staphylococcus aureus: 56.7 × 107 CFU/mL in the blank group and 2.5 × 107 CFU/mL in the 5/5 CPH group; Escherichia coli: 66.0 × 107 CFU/mL in the blank group and 8.5 × 107 CFU/mL in the 5/5 CPH group), and certain adhesion (0.71 kPa in the 5/5 CPH group) properties which can promote wound healing (wound healing reached 98.02% within 14 days in the 5/5 CPH group) and repair of cells with broad application prospects

US Cosmic Visions: New Ideas in Dark Matter 2017: Community Report

This white paper summarizes the workshop "U.S. Cosmic Visions: New Ideas in Dark Matter" held at University of Maryland on March 23-25, 2017.Comment: 102 pages + reference