64 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/15

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Bayesian networks to identify potential high-risk multimorbidity and intervention clusters in inpatients: an explorative data mining study.

Swiss Med Wkly. 2020 Jul 27;150:w20299

Authors: Roth JA, Sakoparnig T, Gerber M, Hug BL

Abstract
AIMS OF THE STUDY: Based on large sets of routine hospital data from inpatient cases, we aimed to explore multimorbidity and intervention clusters showing high risks for in-hospital mortality and unplanned readmissions using data-driven analytical methods.
METHODS: We performed an explorative, historical cohort study of consecutive inpatient cases at a tertiary care centre with an integrated platform for routine healthcare data in Switzerland. From January 2012 through to December 2017, all inpatients aged ≥18 years at hospital admission were eligible for study inclusion. We predefined all-cause in-hospital death and unplanned hospital readmission as co-primary outcomes. In a first step, we explored and visualised multimorbidity and intervention clusters using mutual information analysis. In a subsequent step, we trained multi-layer Bayesian networks to identify clusters associated with in-hospital death and/or unplanned hospital readmission.
RESULTS: Among 190,837 inpatient cases, 7994 unique diagnoses and 6639 interventions were routinely recorded during the six-year study period. Based on the mutual information analysis, we identified 32 multimorbidity clusters and 24 intervention clusters – of which several were directly related to in-hospital mortality and/or unplanned readmission in the subsequent Bayesian network analysis.
CONCLUSIONS: Bayesian network analysis may be used as a tool to mine large healthcare databases in order to explore intervention targets for quality improvement programmes. However, the resulting associations should be substantiated in consecutive investigations using specific causal models. (Trial registration no EKNZ 2016-02128.).

PMID: 32920788 [PubMed - in process]

Gene expression during bacterivorous growth of a widespread marine heterotrophic flagellate.

ISME J. 2020 Sep 12;:

Authors: Massana R, Labarre A, López-Escardó D, Obiol A, Bucchini F, Hackl T, Fischer MG, Vandepoele K, Tikhonenkov DV, Husnik F, Keeling PJ

Abstract
Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models. Our reanalysis of recent molecular datasets revealed that the cultured heterotrophic flagellate Cafeteria burkhardae is widespread in the global oceans, which prompted us to design a transcriptomics study with this species, grown with the cultured flavobacterium Dokdonia sp. We compared the gene expression between exponential and stationary phases, which were complemented with three starvation by dilution phases that appeared as intermediate states. We found distinct expression profiles in each condition and identified 2056 differentially expressed genes between exponential and stationary samples. Upregulated genes at the exponential phase were related to DNA duplication, transcription and translational machinery, protein remodeling, respiration and phagocytosis, whereas upregulated genes in the stationary phase were involved in signal transduction, cell adhesion, and lipid metabolism. We identified a few highly expressed phagocytosis genes, like peptidases and proton pumps, which could be used to target this ecologically relevant process in marine ecosystems.

PMID: 32920602 [PubMed - as supplied by publisher]

Tumor reversion and Embryo morphogenetic factors.

Semin Cancer Biol. 2020 Sep 10;:

Authors: Proietti S, Cucina A, Pensotti A, Fuso A, Marchese C, Nicolini A, Bizzarri M

Abstract
Several studies have shown that cancer cells can be "phenotypically reversed", thus achieving a "tumor reversion", by losing malignant hallmarks as migrating and invasive capabilities. These findings suggest that genome activity can switch to assume a different functional configuration, i.e. a different Gene Regulatory Network pattern. Indeed, once "destabilized", cancer cells enter into a critical transition phase that can be adequately "oriented" by yet unidentified morphogenetic factors - acting on both cells and their microenvironment - that trigger an orchestrated array of structural and epigenetic changes. Such process can bypass genetic abnormalities, through rerouting cells toward a benign phenotype. Oocytes and embryonic tissues, obtained by animals and humans, display such "reprogramming" capability, as a number of yet scarcely identified embryo-derived factors can revert the malignant phenotype of several types of tumors. Mechanisms involved in the reversion process include the modification of cell-microenvironment cross talk (mostly through cytoskeleton reshaping), chromatin opening, demethylation, and epigenetic changes, modulation of biochemical pathways, comprising TCTP-p53, PI3K-AKT, FGF, Wnt, and TGF-β-dependent cascades. Results herein discussed promise to open new perspectives not only in the comprehension of cancer biology but also toward different therapeutic options, as suggested by a few preliminary clinical studies.

PMID: 32920125 [PubMed - as supplied by publisher]

Reduced graphene oxide foam templated by nickel foam for organ-on-a-chip engineering of cardiac constructs.

Mater Sci Eng C Mater Biol Appl. 2020 Dec;117:111344

Authors: Wang Y, Dong Y, Chen P, Chen R, Li Y, Du W, Liu BF

Abstract
Myocardial tissue engineering has attracted increasing awareness for heart failure, and researchers are committed to developing an appropriate biological material to reconstruct myocardial tissues. Here, we applied a simple and high-throughput method to fabricate a three-dimensional (3D) partially reduced graphene oxide (PRGO) foam chip, whose structure, properties and biocompatibility confirmed that it is a suitable material for myocardial tissue engineering. The PRGO foam was produced based on a reduction reaction that occurred at the interface between the graphene oxide (GO) solution and Ni foam; as the Ni foam scaffold was dissolved in an HCl solution, the PRGO foam was harvested. After the PRGO foam was freeze-dried, its elasticity property was evaluated, and primary cardiomyocytes obtained from 2-day-old SD rats were cultured in the 3D foam. The results demonstrated good cell adherence, spreading, activity, organization and beating function in the PRGO foam during the long-term culturing process, which proved that the PRGO foam obtained by this method had application potential for myocardial tissue engineering.

PMID: 32919691 [PubMed - in process]

A noble electrochemical sensor based on TiO2@CuO-N-rGO and poly (L-cysteine) nanocomposite applicable for trace analysis of flunitrazepam.

Mater Sci Eng C Mater Biol Appl. 2020 Dec;117:111300

Authors: Sohouli E, Ghalkhani M, Rostami M, Rahimi-Nasrabadi M, Ahmadi F

Abstract
Flunitrazepam or date rape medication with trade name of Rohypnol belongs to the benzodiazepines branch that is used as a sedative, anesthetic, anticonvulsant, muscle relaxant, and antianxiety drug. It is known as "drug of aggression" because of its very strong and long-lasting effects on the central nervous system. The sedative influence of flunitrazepam drug increases with alcohol drinking, which causes mental and motor disorders and causes the victim to become silent. Due to its criminals use, its accurate measurement is crucial. In this work, a novel electrochemical sensor based on TiO2@CuO-N doped rGO, TiO2@CuO-N-rGO, nano-composite and poly (L-cysteine), poly (L-Cys), is presented for trace analysis of flunitrazepam in aqueous solution. At first, TiO2@CuO-N-rGO nano-composite was synthesized by the sol-gel method and characterized by Raman spectroscopy, Fourier transform infrared, field emission scanning electron microscope, and X-ray diffraction analysis. Then, the suspension of the TiO2@CuO-N-rGO nano-composite was drop casted on the surface of the glassy carbon electrode (GCE/TiO2@CuO-N-rGO). After that, electro-polymerization of l-cysteine on the GCE/TiO2@CuO-N-rGO surface was performed by cyclic voltammetry (CV) method. The electrochemical characteristics of the GCE/TiO2@CuO-N-rGO/poly (L-Cys) surface were evaluated in the solution of ferri/ferrocyanide by electrochemical impedance spectroscopy (EIS) and CV techniques. The increase in current, change in oxidation peak potential, and the appearance of two reduction peaks indicated higher electron transfer rate with well-performed electrochemical process of flunitrazepam at the modified electrode surface compared to the bare GCE. These improvements originate from the synergistic effect of TiO2@CuO-N-rGO nano-composite and poly (L-Cys). Finally, a linear relationship was resulted between the oxidation peak current and the concentration of flunitrazepam in the wide concentration range of 1 nM to 50 μM with a detection limit of 0.3 nM.

PMID: 32919661 [PubMed - in process]

Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria.

Microbiome. 2020 Sep 12;8(1):133

Authors: Seelbinder B, Chen J, Brunke S, Vazquez-Uribe R, Santhaman R, Meyer AC, de Oliveira Lino FS, Chan KF, Loos D, Imamovic L, Tsang CC, Lam RP, Sridhar S, Kang K, Hube B, Woo PC, Sommer MOA, Panagiotou G

Abstract
BACKGROUND: Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing.
RESULTS: While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.
CONCLUSIONS: We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. Video abstract.

PMID: 32919472 [PubMed - in process]

11 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/14

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

62 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/12

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

59 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/12

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

28 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/12

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

56 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/10

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

61 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/09

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/08

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Photoactivatable Cre knock-in mice for spatiotemporal control of genetic engineering in vivo.

Lab Invest. 2020 Sep 05;:

Authors: Yoshimi K, Yamauchi Y, Tanaka T, Shimada T, Sato M, Mashimo T

Abstract
Although the Cre-loxP recombination system has been extensively used to analyze gene function in vivo, spatiotemporal control of Cre activity is a critical limitation for easy and precise recombination. Here, we established photoactivatable-Cre (PA-Cre) knock-in (KI) mice at a safe harbor locus for the spatial and temporal regulation of Cre recombinase activity. The mice showed whole-body Cre recombination activity following light exposure for only 1 h. Almost no leaks of Cre recombination activity were detected in the KI mice under natural light conditions. Spot irradiation could induce locus-specific recombination noninvasively, enabling us to compare phenotypes on the left and right sides in the same mouse. Furthermore, long-term irradiation using an implanted wireless LED substantially improved Cre recombination activity, especially in the brain. These results demonstrate that PA-Cre KI mice can facilitate the spatiotemporal control of genetic engineering and provide a useful resource to elucidate gene function in vivo with Cre-loxP.

PMID: 32892213 [PubMed - as supplied by publisher]

An investigation of the pharmacological applications used for the Ancient Egyptian systemic model 'ra-ib' compared with modern Traditional Chinese Medicine.

J Ethnopharmacol. 2020 Sep 03;:113115

Authors: Russell J, Sun M, Liang W, He M, Schroen Y, Zou W, Pommerening T, Wang M

Abstract
ETHNOPHARMACOLOGICAL RELEVANCE: Ancient Egyptian texts only offer glimpses into their conceptual understandings of the inner-body and illness manifestation. Explanations of how prescribed materia medica were believed to work are rare and obscure, often resulting in modern approximations for ancient terminology such as 'ra-ib'-an ancient Egyptian classification predominantly translated as 'stomach'-leading to misunderstandings of historical texts, and therefore their use of pharmacology.
AIM OF THE STUDY: To investigate the ra-ib and the explanatory models of illness from the Egyptian perspective, and to explore the link between these and the prescribed selection of materia medica. To then compare the conceptual mechanics of these treatment strategies with those of another non-Western tradition-namely Traditional Chinese Medicine (TCM)-to provide further insight into potential conceptual frameworks.
MATERIALS AND METHODS: We conducted a case study of a unit of Ancient Egyptian texts focusing on the ra-ib. Totalling 34 prescriptions, the first stage lexicographically analysed the texts using cognitive linguistic and translation theories to produce our new understanding. This enabled our comparison of the mechanics of materia medica usage within these texts with those found in TCM outlined by the Pharmacopoeia of the Peoples Republic of Pharmacopeia of the People's Republic of China2015 for the relevant ingredients.
RESULTS: the study demonstrated that-rather than denoting the organ 'stomach'-ra-ib instead constitutes a system running from the mouth, downward to the anus. This is best translated as 'inner thoroughfare', and changes the way in which we attempt to understand potential motivations in the selection of ingredients. By exploring common themes in the use of eleven securely translated ingredients from the Egyptian corpus and the Pharmacopoeia of the People's Republic of China-representing a modern traditional system which understands the body via a series of interconnected systems-we were able to highlight certain themes which might be 'universal' to system-based traditions; this provided new insights into the Egyptian motivations for treatment selection.
CONCLUSIONS: Having gained the ancient view of the body and illness, cultural comparisons are important for providing further potential insights and clarifications of a discontinued historical healing tradition. The new understanding of the ra-ib from our study greatly changes the way in which we understand the dynamics of Egyptian ethnopharmacological source material from this period.

PMID: 32891812 [PubMed - as supplied by publisher]

A narrative literature review on traditional medicine options for treatment of corona virus disease 2019 (COVID-19).

Complement Ther Clin Pract. 2020 Aug;40:101214

Authors: Mirzaie A, Halaji M, Dehkordi FS, Ranjbar R, Noorbazargan H

Abstract
Coronavirus disease 2019 (COVID-19) as a life-threatening disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is accounted as global public health concern. Treatment of COVID-19 is primarily supportive and the role of antiviral agents is yet to be established. However, there are no specific anti-COVID-19 drugs and vaccine until now. This review focuses on traditional medicine such as medicinal plant extracts as promising approaches against COVID-19. Chinese, Indian and Iranian traditional medicine, suggests some herbs for prevention, treatment and rehabilitation of the diseases including COVID-19. Although, inhibition of viral replication is considered as general mechanism of herbal extracts, however some studies demonstrated that traditional herbal extracts can interact with key viral proteins which are associated with virus virulence. Chinese, Indian and Iranian traditional medicine, suggests some herbs for prevention, treatment and rehabilitation of the diseases including COVID-19. However the beneficial effects of these traditional medicines and their clinical trials remained to be known. Herein, we reviewed the latest updates on traditional medicines proposed for treatment of COVID-19.

PMID: 32891290 [PubMed - in process]

Organoids Model Transcriptional Hallmarks of Oncogenic KRAS Activation in Lung Epithelial Progenitor Cells.

Cell Stem Cell. 2020 Aug 22;:

Authors: Dost AFM, Moye AL, Vedaie M, Tran LM, Fung E, Heinze D, Villacorta-Martin C, Huang J, Hekman R, Kwan JH, Blum BC, Louie SM, Rowbotham SP, Sainz de Aja J, Piper ME, Bhetariya PJ, Bronson RT, Emili A, Mostoslavsky G, Fishbein GA, Wallace WD, Krysan K, Dubinett SM, Yanagawa J, Kotton DN, Kim CF

Abstract
Mutant KRAS is a common driver in epithelial cancers. Nevertheless, molecular changes occurring early after activation of oncogenic KRAS in epithelial cells remain poorly understood. We compared transcriptional changes at single-cell resolution after KRAS activation in four sample sets. In addition to patient samples and genetically engineered mouse models, we developed organoid systems from primary mouse and human induced pluripotent stem cell-derived lung epithelial cells to model early-stage lung adenocarcinoma. In all four settings, alveolar epithelial progenitor (AT2) cells expressing oncogenic KRAS had reduced expression of mature lineage identity genes. These findings demonstrate the utility of our in vitro organoid approaches for uncovering the early consequences of oncogenic KRAS expression. This resource provides an extensive collection of datasets and describes organoid tools to study the transcriptional and proteomic changes that distinguish normal epithelial progenitor cells from early-stage lung cancer, facilitating the search for targets for KRAS-driven tumors.

PMID: 32891189 [PubMed - as supplied by publisher]

D1 receptors in the anterior cingulate cortex modulate basal mechanical sensitivity threshold and glutamatergic synaptic transmission.

Mol Brain. 2020 Sep 05;13(1):121

Authors: Darvish-Ghane S, Quintana C, Beaulieu JM, Martin LJ

Abstract
The release of dopamine (DA) into target brain areas is considered an essential event for the modulation of many physiological effects. While the anterior cingulate cortex (ACC) has been implicated in pain related behavioral processes, DA modulation of synaptic transmission within the ACC and pain related phenotypes remains unclear. Here we characterized a Crispr/Cas9 mediated somatic knockout of the D1 receptor (D1R) in all neuronal subtypes of the ACC and find reduced mechanical thresholds, without affecting locomotion and anxiety. Further, the D1R high-efficacy agonist SKF 81297 and low efficacy agonist (±)-SKF-38393 inhibit α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic receptor (AMPAR) currents in the ACC. Paradoxically, the D1R antagonists SCH-23390 and SCH 33961 when co-applied with D1R agonists produced a robust short-term synergistic depression of AMPAR currents in the ACC, demonstrating an overall inhibitory role for D1R ligands. Overall, our data indicate that absence of D1Rs in the ACC enhanced peripheral sensitivity to mechanical stimuli and D1R activation decreased glutamatergic synaptic transmission in ACC neurons.

PMID: 32891169 [PubMed - in process]

23 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:

"systems biology"

These pubmed results were generated on 2020/09/06

PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.