LIVIVO - Search results -

Search results

Result 1 - 10 of total 131

Search options

Article ; Online: Advances in AI for Protein Structure Prediction: Implications for Cancer Drug Discovery and Development.

Qiu, Xinru / Li, Han / Ver Steeg, Greg / Godzik, Adam

2024 Volume 14, Issue 3

Abstract: Recent advancements in AI-driven technologies, particularly in protein structure prediction, are significantly reshaping the landscape of drug discovery and development. This review focuses on the question of how these technological breakthroughs, ... ...

Abstract	Recent advancements in AI-driven technologies, particularly in protein structure prediction, are significantly reshaping the landscape of drug discovery and development. This review focuses on the question of how these technological breakthroughs, exemplified by AlphaFold2, are revolutionizing our understanding of protein structure and function changes underlying cancer and improve our approaches to counter them. By enhancing the precision and speed at which drug targets are identified and drug candidates can be designed and optimized, these technologies are streamlining the entire drug development process. We explore the use of AlphaFold2 in cancer drug development, scrutinizing its efficacy, limitations, and potential challenges. We also compare AlphaFold2 with other algorithms like ESMFold, explaining the diverse methodologies employed in this field and the practical effects of these differences for the application of specific algorithms. Additionally, we discuss the broader applications of these technologies, including the prediction of protein complex structures and the generative AI-driven design of novel proteins.
MeSH term(s)	Humans ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Neoplasms/drug therapy ; Drug Discovery ; Drug Development ; Artificial Intelligence
Chemical Substances	Antineoplastic Agents
Language	English
Publishing date	2024-03-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom14030339
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: Unusual structural and functional features of TpLRR/BspA-like LRR proteins.

Takkouche, Abraham / Qiu, Xinru / Sedova, Mayya / Jaroszewski, Lukasz / Godzik, Adam

Journal of structural biology

2023 Volume 215, Issue 3, Page(s) 108011

Abstract: Leucine Rich Repeat (LRR) domains, are present in hundreds of thousands of proteins across all kingdoms of life and are typically involved in protein-protein interactions and ligand recognition. LRR domains are classified into eight classes and when ... ...

Abstract	Leucine Rich Repeat (LRR) domains, are present in hundreds of thousands of proteins across all kingdoms of life and are typically involved in protein-protein interactions and ligand recognition. LRR domains are classified into eight classes and when examined in three dimensions seven, of them form curved solenoid-like super-helices, also described as toruses, with a beta sheet on the concave (inside) and stacked alpha-helices on the convex (outside) of the torus. Here we present an overview of the least characterized 8th class of LRR proteins, the TpLRR-like LRRs, named after the Treponema pallidum protein Tp0225. Proteins from the TpLRR class differ from the proteins in all other known LRR classes by having a flipped curvature, with the beta sheet on the convex side of the torus and irregular secondary structure instead of helices on the opposite, now concave site. TpLRR proteins also present highly divergent sequence pattern of individual repeats and can associate with specific types of additional domains. Several of the characterized proteins from this class, specifically the BspA-like proteins, were found in human bacterial and protozoan pathogens, playing an important role in the interactions between the pathogens and the host immune system. In this paper we surveyed all existing experimental structures and selected AlphaFold models of the best-known proteins containing this class of LRR repeats, analyzing the relation between the pattern of conserved residues, specific structural features and functions of these proteins.
MeSH term(s)	Humans ; Leucine-Rich Repeat Proteins ; Proteins/chemistry ; Protein Domains ; Protein Structure, Secondary ; Bacteria/chemistry
Chemical Substances	Leucine-Rich Repeat Proteins ; Proteins
Language	English
Publishing date	2023-08-09
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2023.108011
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 1428: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Triple kill: DDR inhibitors, radiotherapy and immunotherapy leave cancer cells with no escape.

Qiu, Yuyue / Hu, Xinru / Zeng, Xiaoping / Wang, Hongmei

Acta biochimica et biophysica Sinica

2022 Volume 54, Issue 11, Page(s) 1569–1576

Abstract: Radiotherapy (RT) has been widely used in the clinical treatment of cancers, but radiotherapy resistance (RR) leads to RT failure, tumor recurrence and metastasis. Many studies have been performed on the potential mechanisms behind RR, and a strong link ... ...

Abstract	Radiotherapy (RT) has been widely used in the clinical treatment of cancers, but radiotherapy resistance (RR) leads to RT failure, tumor recurrence and metastasis. Many studies have been performed on the potential mechanisms behind RR, and a strong link has been found between RR and DNA damage. RT-induced DNA damage triggers a protective mechanism called the DNA damage response (DDR). DDR consists of several aspects, including the detection of DNA damage and induction of cell cycle checkpoint, DNA repair, and eventual induction of cell death. A large number of studies have shown that DDR inhibition leads to significantly enhanced sensitivity of cancer cells to RT. DDR may be an effective target for radio- and chemo-sensitization during cancer treatment. Therefore, many inhibitors of important enzymes involved in the DDR have been developed, such as PARP inhibitors, DNA-PK inhibitors, and ATM/ATR inhibitors. In addition, DNA damage also triggers the cGAS-STING signaling pathway and the ATM/ATR (CHK)/STAT pathway to induce immune infiltration and T-cell activation. This review discusses the effects of DDR pathway dysregulation on the tumor response to RT and the strategies for targeting these pathways to increase tumor susceptibility to RT. Finally, the potential for the combination treatment of radiation, DDR inhibition, and immunotherapy is described.
MeSH term(s)	Humans ; Ataxia Telangiectasia Mutated Proteins/genetics ; Ataxia Telangiectasia Mutated Proteins/metabolism ; Neoplasm Recurrence, Local ; DNA Damage ; DNA Repair ; Immunotherapy
Chemical Substances	Ataxia Telangiectasia Mutated Proteins (EC 2.7.11.1)
Language	English
Publishing date	2022-10-27
Publishing country	China
Document type	Review ; Journal Article
ZDB-ID	2175256-4
ISSN	1745-7270 ; 0582-9879 ; 1672-9145
ISSN (online)	1745-7270
ISSN	0582-9879 ; 1672-9145
DOI	10.3724/abbs.2022153
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Exosomes reveal the dual nature of radiotherapy in tumor immunology.

Hu, Xinru / Qiu, Yuyue / Zeng, Xiaoping / Wang, Hongmei

Cancer science

2022 Volume 113, Issue 4, Page(s) 1105–1112

Abstract: Radioresistance is the potential cause of cancer metastasis and recurrence. Radiation-induced changes in exosomes can partially explain the undesirable prognosis of radiotherapy (RT). Exosomes, newly discovered ways of cell communication, carry the ... ...

Abstract	Radioresistance is the potential cause of cancer metastasis and recurrence. Radiation-induced changes in exosomes can partially explain the undesirable prognosis of radiotherapy (RT). Exosomes, newly discovered ways of cell communication, carry the characteristics of their origin, resulting in their diversity. Various exosomes in the tumor microenvironment exert different function in immune response. In this review, the dual effect of RT on the immune system was described, and the effect of radiotherapy on tumors via exosomes was explored. The molecules in exosomes after RT were described to play immunosuppressive and immunocompetent roles: immune-related receptors and cell signaling molecules involved in both adaptive and innate immune system were present. CD69, TIGIT, TIM-3, LAG-3 and the tumor necrosis factor (TNF) family that signal to T cells were shown to be regulated by exosomes after irradiation. The change in innate immunity-derived like receptors, Leukocyte Immunoglobin-Like Receptors (LILR) was described, as well as B7-H3, V-domain containing Ig suppressor of T cell activation (VISTA), and CD155 on tumor cells. These changed molecules inhibit and activate the immune system through different mechanisms. By analyzing the relationship between exosome-derived molecules and immunity, this review shows that radiotherapy can induce immunosuppression and immune clearance through exosomes, thereby treating tumors and improving patient prognosis.
MeSH term(s)	Cell Communication ; Exosomes ; Humans ; Neoplasms/pathology ; Prognosis ; Tumor Microenvironment
Language	English
Publishing date	2022-03-07
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2115647-5
ISSN	1349-7006 ; 1349-7006
ISSN (online)	1349-7006
ISSN	1349-7006
DOI	10.1111/cas.15314
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Group 1 metabotropic glutamate receptor expression defines a T cell memory population during chronic Toxoplasma infection that enhances IFN-gamma and perforin production in the CNS.

Vizcarra, Edward A / Ulu, Arzu / Landrith, Tyler A / Qiu, Xinru / Godzik, Adam / Wilson, Emma H

Brain, behavior, and immunity

2023 Volume 114, Page(s) 131–143

Abstract: Within the brain, a pro-inflammatory response is essential to prevent clinical disease due to Toxoplasma gondii reactivation. Infection in the immunocompromised leads to lethal Toxoplasmic encephalitis while in the immunocompetent, there is persistent ... ...

Abstract	Within the brain, a pro-inflammatory response is essential to prevent clinical disease due to Toxoplasma gondii reactivation. Infection in the immunocompromised leads to lethal Toxoplasmic encephalitis while in the immunocompetent, there is persistent low-grade inflammation which is devoid of clinical symptoms. This signifies that there is a well-balanced and regulated inflammatory response to T. gondii in the brain. T cells are the dominant immune cells that prevent clinical disease, and this is mediated through the secretion of effector molecules such as perforins and IFN-γ. The presence of cognate antigen, the expression of survival cytokines, and the alteration of the epigenetic landscape drive the development of memory T cells. However, specific extrinsic signals that promote the formation and maintenance of memory T cells within tissue are poorly understood. During chronic infection, there is an increase in extracellular glutamate that, due to its function as an excitatory neurotransmitter, is normally tightly controlled in the CNS. Here we demonstrate that CD8
Language	English
Publishing date	2023-08-20
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	639219-2
ISSN	1090-2139 ; 0889-1591
ISSN (online)	1090-2139
ISSN	0889-1591
DOI	10.1016/j.bbi.2023.08.015
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2276: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 327: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Defect-induced charge redistribution of MoO

Yu, Xinru / Qiu, Peng / Wang, Yongchao / He, Bing / Xu, Xiangran / Zhu, Huiling / Ding, Jian / Liu, Xueqin / Li, Zhen / Wang, Yang

Journal of colloid and interface science

2023 Volume 640, Page(s) 775–782

Abstract: Photocatalytic ammonia synthesis technology has become one of the effective methods to replace the Haber method for nitrogen fixation in the future for its low energy consumption and green environment. However, limited by the weak adsorption/activation ... ...

Abstract	Photocatalytic ammonia synthesis technology has become one of the effective methods to replace the Haber method for nitrogen fixation in the future for its low energy consumption and green environment. However, limited by the weak adsorption/activation ability of N
Language	English
Publishing date	2023-03-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	241597-5
ISSN	1095-7103 ; 0021-9797
ISSN (online)	1095-7103
ISSN	0021-9797
DOI	10.1016/j.jcis.2023.03.010
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Bonn / Germany

Z 71/707: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Gender differences in smoking-induced changes in the tumor immune microenvironment.

Alisoltani, Arghavan / Qiu, Xinru / Jaroszewski, Lukasz / Sedova, Mayya / Iyer, Mallika / Godzik, Adam

Archives of biochemistry and biophysics

2023 Volume 739, Page(s) 109579

Abstract: Both gender and smoking are correlated with prevalence and outcomes in many types of cancers. Tobacco smoke is a known carcinogen through its genotoxicity but can also affect cancer progression through its effect on the immune system. In this study, we ... ...

Abstract	Both gender and smoking are correlated with prevalence and outcomes in many types of cancers. Tobacco smoke is a known carcinogen through its genotoxicity but can also affect cancer progression through its effect on the immune system. In this study, we aim to evaluate the hypothesis that the effects of smoking on the tumor immune microenvironment will be influenced differently by gender using large-scale analysis of publicly available cancer datasets. We used The Cancer Genomic Atlas (TCGA) datasets (n = 2724) to analyze effects of smoking on different cancer immune subtypes and the relative abundance of immune cell types between male and female cancer patients. We further validated our results by analyzing additional datasets, including Expression Project for Oncology (expO) bulk RNA-seq dataset (n = 1118) and single-cell RNA-seq dataset (n = 14). Results of our study indicate that in female patients, two immune subtypes, C1 and C2, are respectively over and under abundant in smokers vs. never smokers. In males, the only significant difference is underabundance of the C6 subtype in smokers. We identified gender-specific differences in the population of immune cell types between smokers and never smokers in all TCGA and expO cancer types. Increased plasma cell population was identified as the most consistent feature distinguishing smokers and never smokers, especially in current female smokers based on both TCGA and expO data. Our analysis of existing single-cell RNA-seq data further revealed that smoking differentially affects the gene expression profile of cancer patients based on the immune cell type and gender. In our analysis, female and male smokers show different smoking-induced patterns of immune cells in tumor microenvironment. Besides, our results suggest cancer tissues directly exposed to tobacco smoke undergo the most significant changes, but all other tissue types are affected as well. Findings of current study also indicate that changes in the populations of plasma cells and their correlations to survival outcomes are stronger in female current smokers, with implications for cancer immunotherapy of women smokers. In conclusion, results of this study can be used to develop personalized treatment plans for cancer patients who smoke, particularly women smokers, taking into account the unique immune cell profile of their tumors.
MeSH term(s)	Humans ; Male ; Female ; Tumor Microenvironment ; Sex Factors ; Tobacco Smoke Pollution ; Smoking/adverse effects ; Lung Neoplasms/pathology
Chemical Substances	Tobacco Smoke Pollution
Language	English
Publishing date	2023-03-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	523-x
ISSN	1096-0384 ; 0003-9861
ISSN (online)	1096-0384
ISSN	0003-9861
DOI	10.1016/j.abb.2023.109579
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Uc I Zs.237: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Improving grindability and bioaccessibility of chicken bone by in situ steam explosion

Kong, Feng / Li, Yue / Li, Pengfei / Qiu, Xinru / Guo, Xingfeng / Chen, Jinfa / Wang, Wenhao

International Journal of Food Science & Technology. 2023 June, v. 58, no. 6 p.3201-3208

2023

Abstract: The impacts of in situ steam explosion (ISE) on the particle size, protein solubility and digestibility, calcium release and structural characteristics of chicken bone powder were analysed. ISE significantly reduced the average particle size from 142.62 ... ...

Abstract	The impacts of in situ steam explosion (ISE) on the particle size, protein solubility and digestibility, calcium release and structural characteristics of chicken bone powder were analysed. ISE significantly reduced the average particle size from 142.62 to 84.47–105.10 μm, while maintained the proximate compositions. The Fourier transforms infrared spectra and X‐ray diffraction further illustrated that there were no marked differences in the functional groups between native and ISE bone powders. Moreover, soluble protein content in chicken bone powder was remarkably enhanced by the ISE from 3.28 to 3.73 mg g⁻¹. ISE powder (at 121 °C for 90 min) had higher protein digestibility (48.63%) than that of native (30.82%). Finally, ISE powder showed a higher calcium release and 2,2′‐azino‐bis (3‐ethylbenzothiazoline‐6‐sulphonic acid) diammonium salt (ABTS) radical scavenging activity of digestive juice. The results proposed the feasibility of using ISE as an effective strategy to improve the nutritional quality of chicken bone.
Keywords	X-ray diffraction ; bioavailability ; calcium ; chickens ; digestibility ; digestible protein ; digestive juices ; particle size ; protein content ; protein solubility ; technology
Language	English
Dates of publication	2023-06
Size	p. 3201-3208.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	883561-5
ISSN	0950-5423
ISSN	0950-5423
DOI	10.1111/ijfs.16452
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 2121: Show issues

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Deciphering Abnormal Platelet Subpopulations in Inflammatory Diseases through Machine Learning and Single-Cell Transcriptomics

Qiu, Xinru / Nair, Meera G. / Jaroszewski, Lukasz / Godzik, Adam

bioRxiv

Abstract: Introduction: The transcriptional heterogeneity of activated platelets, play a significant role in contributing to negative outcomes in sepsis, COVID-19, and autoimmune diseases such as systemic lupus erythematosus (SLE). Despite this, our understanding ... ...

Abstract	Introduction: The transcriptional heterogeneity of activated platelets, play a significant role in contributing to negative outcomes in sepsis, COVID-19, and autoimmune diseases such as systemic lupus erythematosus (SLE). Despite this, our understanding of these heterogeneous platelet responses remains limited. In this study, we aim to investigate the diverse transcriptional profiles of activated platelets in these diseases, with the goal of deciphering this platelet heterogeneity for new therapeutic strategies to target abnormal and pathogenic platelet subtypes. Materials and methods: We obtained the single cell transcriptional profiles of blood platelets from patients with COVID-19, sepsis, and SLE. Utilizing machine learning algorithms, Deep Neural Network (DNN) and eXtreme Gradient Boosting (XGB), we discerned the distinct transcriptomic signatures indicative of fatal versus survival clinical outcomes. Our methodological framework incorporated source data annotations and platelet markers and used SingleR and Seurat for detailed profiling. Additionally, we implemented Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and visualization, aiding in the detection of various platelet subtypes and their correlation with disease status and patient outcomes. Results: Our study identified distinct platelet subpopulations that are associated with disease severity. We demonstrated that alterations in platelet transcription patterns can exacerbate endotheliopathy, potentially heightening the risk of coagulation in fatal patients. Moreover, these changes can also influence lymphocyte function, indicating a more extensive role for platelets in inflammatory and immune responses. Conclusions: Enhanced transcriptional heterogeneity in activated platelets is linked to adverse outcomes in conditions such as sepsis, COVID-19, and autoimmune diseases. The discovery of these unique platelet subpopulations paves the way for innovative therapeutic strategies targeting platelet activation, which could potentially improve patient outcomes.
Keywords	covid19
Language	English
Publishing date	2023-12-21
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.12.20.572680
Database	COVID19

Full text online

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Photonic-electronic integrated circuit-based coherent LiDAR engine.

Lukashchuk, Anton / Yildirim, Halil Kerim / Bancora, Andrea / Lihachev, Grigory / Liu, Yang / Qiu, Zheru / Ji, Xinru / Voloshin, Andrey / Bhave, Sunil A / Charbon, Edoardo / Kippenberg, Tobias J

Nature communications

2024 Volume 15, Issue 1, Page(s) 3134

Abstract: Chip-scale integration is a key enabler for the deployment of photonic technologies. Coherent laser ranging or FMCW LiDAR, a perception technology that benefits from instantaneous velocity and distance detection, eye-safe operation, long-range, and ... ...

Abstract	Chip-scale integration is a key enabler for the deployment of photonic technologies. Coherent laser ranging or FMCW LiDAR, a perception technology that benefits from instantaneous velocity and distance detection, eye-safe operation, long-range, and immunity to interference. However, wafer-scale integration of these systems has been challenged by stringent requirements on laser coherence, frequency agility, and the necessity for optical amplifiers. Here, we demonstrate a photonic-electronic LiDAR source composed of a micro-electronic-based high-voltage arbitrary waveform generator, a hybrid photonic circuit-based tunable Vernier laser with piezoelectric actuators, and an erbium-doped waveguide amplifier. Importantly, all systems are realized in a wafer-scale manufacturing-compatible process comprising III-V semiconductors, silicon nitride photonic integrated circuits, and 130-nm SiGe bipolar complementary metal-oxide-semiconductor (CMOS) technology. We conducted ranging experiments at a 10-meter distance with a precision level of 10 cm and a 50 kHz acquisition rate. The laser source is turnkey and linearization-free, and it can be seamlessly integrated with existing focal plane and optical phased array LiDAR approaches.
Language	English
Publishing date	2024-04-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47478-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

In stock of ZB MED Bonn / Germany

Order via subito

Inter-library loan at ZB MED

Full text online

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito