We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment ...indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets,
N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
Critical cases of coronavirus disease 2019 (COVID‐19) are associated with a high risk of mortality. It remains unclear why patients with the same critical condition have different outcomes. We aimed ...to explore relevant factors that may affect the prognosis of critical COVID‐19 patients. Six critical COVID‐19 inpatients were included in our study. The six patients were divided into two groups based on whether they had a good or poor prognosis. We collected peripheral blood samples at admission and the time point of exacerbation to compare differences in the phenotypes and functions of major populations of immune cells between the groups. On admission, compared to patients with poor prognoses, those with good prognoses had significantly higher counts of monocytes (P < .05), macrophages (P < .05), higher frequency of CD3+CD4+CD45RO+CXCR3+ subsets (P < .05), higher frequency of CD14+CD11C+HLA‐DR+ subset of dendritic cells (P < .05), and a lower count of neutrophils (P < .05). At the time point of exacerbation, the proportions of naïve CD4+ T cells (P < .05), Tregs, and Th2 cells in the poor prognosis group were relatively higher than those in the good prognosis group, and CD4+ memory T cells were relatively lower (P < .05). According to our results, the poor prognosis group showed a worse immune response than the good prognosis group at the time of admission and at exacerbation. Dysregulation of the immune response affects the outcome of critical COVID‐19 patients.
Highlights
The pathogenesis of COVID‐19 is not fully known.
COVID‐19 patients with the same critical condition had different outcomes.
Immune response plays an important role in defensing against virus infections.
Objective
To assess the efficacy of intensive acupuncture (3 times weekly for 8 weeks) versus sham acupuncture for knee osteoarthritis (OA).
Methods
In this multicenter, randomized, sham‐controlled ...trial, patients with knee OA were randomly assigned to receive electroacupuncture (EA), manual acupuncture (MA), or sham acupuncture (SA) 3 times weekly for 8 weeks. Participants, outcome assessors, and statisticians were blinded with regard to treatment group assignment. The primary outcome measure was response rate, which is the proportion of participants who simultaneously achieved minimal clinically important improvement in pain and function by week 8. The primary analysis was conducted using a Z test for proportions in the modified intent‐to‐treat population, which included all randomized participants who had ≥1 post‐baseline measurement.
Results
Of the 480 participants recruited in the trial, 442 were evaluated for efficacy. The response rates at week 8 were 60.3% (91 of 151), 58.6% (85 of 145), and 47.3% (69 of 146) in the EA, MA, and SA groups, respectively. The between‐group differences were 13.0% (97.5% confidence interval 97.5% CI 0.2%, 25.9%; P = 0.0234) for EA versus SA and 11.3% (97.5% CI −1.6%, 24.4%; P = 0.0507) for MA versus SA. The response rates in the EA and MA groups were both significantly higher than those in the SA group at weeks 16 and 26.
Conclusion
Among patients with knee OA, intensive EA resulted in less pain and better function at week 8, compared with SA, and these effects persisted though week 26. Intensive MA had no benefit for knee OA at week 8, although it showed benefits during follow‐up.
An overview of COVID-19 Shi, Yu; Wang, Gang; Cai, Xiao-peng ...
Journal of Zhejiang University. B. Science,
05/2020, Letnik:
21, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Pneumonia caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection emerged in Wuhan City, Hubei Province, China in December 2019. By Feb. 11, 2020, the World Health ...Organization (WHO) officially named the disease resulting from infection with SARS-CoV-2 as coronavirus disease 2019 (COVID-19). COVID-19 represents a spectrum of clinical manifestations that typically include fever, dry cough, and fatigue, often with pulmonary involvement. SARS-CoV-2 is highly contagious and most individuals within the population at large are susceptible to infection. Wild animal hosts and infected patients are currently the main sources of disease which is transmitted via respiratory droplets and direct contact. Since the outbreak, the Chinese government and scientific community have acted rapidly to identify the causative agent and promptly shared the viral gene sequence, and have carried out measures to contain the epidemic. Meanwhile, recent research has revealed critical aspects of SARS-CoV-2 biology and disease pathogenesis; other studies have focused on epidemiology, clinical features, diagnosis, management, as well as drug and vaccine development. This review aims to summarize the latest research findings and to provide expert consensus. We will also share ongoing efforts and experience in China, which may provide insight on how to contain the epidemic and improve our understanding of this emerging infectious disease, together with updated guidance for prevention, control, and critical management of this pandemic.
Various clean energy storage and conversion systems highly depend on rational design of efficient electrocatalysts for oxygen reactions. Increasing both gas molecular diffusion and intrinsic activity ...is critical to boosting its efficiency for bifunctional oxygen electrocatalysis. However, controllable synthesis of catalysts that combines gas molecular diffusion and intrinsic activity remains a fundamental challenge. Herein, a two‐step synthetic strategy is adopted to fabricate a composite oxygen reduction reaction (ORR)/oxygen evolution reaction (OER) bifunctional catalyst (P‐Ag‐Co(OH)2), of which, atomic Ag is anchored in reactive oxygen atoms around nanopores of Co(OH)2 nanosheets. Abundant nanopores provide enough gas molecular diffusion channels, and the special Ag‐O‐Co‐OH catalytic groups around nanopores display high intrinsic catalytic activity, which jointly result in an excellent ORR/OER performance. In alkaline electrolyte, P‐Ag‐Co(OH)2 displays a high half‐wave potential (0.902 V versus RHE) for ORR, and a low overpotential (235 mV at 10 mA cm−2) for OER, which is superior to non‐noble catalysts in previous studies and Pt/C (Ir/C) catalyst. At the same time, the single‐cell zinc‐air battery is prepared with an extremely high discharge peak power density of 435 mW cm−2 and excellent discharge–charge cycle stability.
Porous Ag‐Co(OH)2 nanosheets can completely change the nonactive Co(OH)2 nanosheets in bifunctional oxygen evolution reaction/oxygen evolution reaction catalysis, giving birth to a novel catalyst with high activity and long‐term durability, which demonstrates that the combination of optimization for catalyst structure and regulation for catalytic activity is a powerful strategy to design electrocatalysts with excellent performance.
Proteins must be sorted to specific subcellular compartments to perform their functions. Abnormal protein subcellular localizations are related to many diseases. Although many efforts have been made ...in predicting protein subcellular localization from various static information, including sequences, structures and interactions, such static information cannot predict protein mis-localization events in diseases. On the contrary, the IHC (immunohistochemistry) images, which have been widely applied in clinical diagnosis, contains information that can be used to find protein mis-localization events in disease states. In this study, we create the Vislocas method, which is capable of finding mis-localized proteins from IHC images as markers of cancer subtypes. By combining CNNs and vision transformer encoders, Vislocas can automatically extract image features at both global and local level. Vislocas can be trained with full-sized IHC images from scratch. It is the first attempt to create an end-to-end IHC image-based protein subcellular location predictor. Vislocas achieved comparable or better performances than state-of-the-art methods. We applied Vislocas to find significant protein mis-localization events in different subtypes of glioma, melanoma and skin cancer. The mis-localized proteins, which were found purely from IHC images by Vislocas, are in consistency with clinical or experimental results in literatures. All codes of Vislocas have been deposited in a Github repository (https://github.com/JingwenWen99/Vislocas). All datasets of Vislocas have been deposited in Zenodo (https://zenodo.org/records/10632698).
Vislocas combines vision transformers and CNNs together to extract features from IHC images at both global and local level. The images are automatically augmented before entering Vislocas. Vislocas can be trained with full-sized IHC images in an end-to-end fashion. It can be used to find significant protein translocation events in different cancer subtypes. Display omitted
•Vislocas combines vision transformers and CNNs to extract local and global features from IHC images.•Vislocas can be trained with full-sized IHC images from scratch in an end-to-end fashion.•We reported a list of significant protein translocation evens in different subtypes of glioma, melanoma, and skin cancer.
O-linked β-D-N-acetylglucosamine (O-GlcNAc), as a posttranslational modification (PTM), is a reversible reaction that attaches β-N-GlcNAc to Ser/Thr residues on specific proteins by O-GlcNAc ...transferase (OGT). O-GlcNAcase (OGA) removes the O-GlcNAc from O-GlcNAcylated proteins. O-GlcNAcylation regulates numerous cellular processes, including signal transduction, the cell cycle, metabolism, and energy homeostasis. Dysregulation of O-GlcNAcylation contributes to the development of various diseases, including cancers. Accumulating evidence has revealed that higher expression levels of OGT and hyper-O-GlcNAcylation are detected in many cancer types and governs glucose metabolism, proliferation, metastasis, invasion, angiogenesis, migration and drug resistance. In this review, we describe the biological functions and molecular mechanisms of OGT- or O-GlcNAcylation-mediated tumorigenesis. Moreover, we discuss the potential role of O-GlcNAcylation in tumor immunotherapy. Furthermore, we highlight that compounds can target O-GlcNAcylation by regulating OGT to suppress oncogenesis. Taken together, targeting protein O-GlcNAcylation might be a promising strategy for the treatment of human malignancies.
•Dysregulation of O-GlcNAcylation participates into the tumorigenesis and progression.•O-GlcNAcylation plays a pivotal role in tumor immunotherapy.•Compounds target O-GlcNAcylation by regulating OGT to suppress oncogenesis.•Targeting protein O-GlcNAcylation might be a promising strategy for cancer treatment.
Metal‐oxo clusters have emerged as advanced proton conductors with well‐defined and tunable structures. Nevertheless, the exploitation of metal‐oxo clusters with high and stable proton conductivity ...over a relatively wide temperature range still remains a great challenge. Herein, three sulfate groups decorated zirconium‐oxo clusters (Zr6, Zr18, and Zr70) as proton conductors are reported, which exhibit ultrahigh bulk proton conductivities of 1.71 × 10−1, 2.01 × 10−2, and 3.73 × 10−2 S cm−1 under 70 °C and 98% relative humidity (RH), respectively. Remarkably, Zr6 and Zr70 with multiple sulfate groups as proton hopping sites show ultralow activation energies of 0.22 and 0.18 eV, respectively, and stable bulk conductivities of >10−2 S cm−1 between 30 and 70 °C at 98% RH. Moreover, a time‐dependent proton conductivity test reveals that the best performing Zr6 can maintain high proton conductivity up to 15 h with negligible loss at 70 °C and 98% RH, representing one of the best crystalline cluster‐based proton conducting materials.
Three zirconium‐oxo clusters decorated by sulfate groups, named Zr6, Zr18 and Zr70 are developed as proton conductors with superprotonic conductivities. Zr6 and Zr70 have stable proton conductivities of > 10−2 S cm−1 with ultralow activation energies between 30 and 70 °C, which is the first observed among metal‐oxo cluster‐based proton conductors reported thus far.
Ischemic stroke is the major type of cerebrovascular disease usually resulting in death or disability among the aging population globally. Oxidative stress has been closely linked with ischemic ...stroke. Disequilibrium between excessive production of reactive oxygen species (ROS) and inherent antioxidant capacity leads to subsequent oxidative damage in the pathological progression of ischemic brain injury. Acupuncture has been applied widely in treating cerebrovascular diseases from time immemorial in China. This review mainly lays stress on the evidence to illuminate the possible mechanisms of acupuncture therapy in treating ischemic stroke through regulating oxidative stress. We found that by regulating a battery of molecular signaling pathways involved in redox modulation, acupuncture not only activates the inherent antioxidant enzyme system but also inhibits the excessive generation of ROS. Acupuncture therapy possesses the potential in alleviating oxidative stress caused by cerebral ischemia, which may be linked with the neuroprotective effect of acupuncture.
Recollection is thought to be the hallmark of episodic memory. Here we provide evidence that the hippocampus binds together the diverse elements forming an event, allowing holistic recollection via ...pattern completion of all elements. Participants learn complex 'events' from multiple overlapping pairs of elements, and are tested on all pairwise associations. At encoding, element 'types' (locations, people and objects/animals) produce activation in distinct neocortical regions, while hippocampal activity predicts memory performance for all within-event pairs. When retrieving a pairwise association, neocortical activity corresponding to all event elements is reinstated, including those incidental to the task. Participant's degree of incidental reinstatement correlates with their hippocampal activity. Our results suggest that event elements, represented in distinct neocortical regions, are bound into coherent 'event engrams' in the hippocampus that enable episodic recollection--the re-experiencing or holistic retrieval of all aspects of an event--via a process of hippocampal pattern completion and neocortical reinstatement.
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