31 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 2020/04/10

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.

105 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 2020/04/09

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.

30 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 2020/04/08

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.

15 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 2020/04/07

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.

15 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 2020/04/07

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.

Comparison of GeneChip, nCounter and real-time polymerase chain reaction based gene expressions predicting loco-regional tumour control after primary and postoperative radiochemotherapy in head and neck squamous cell carcinoma.

J Mol Diagn. 2020 Apr 02;:

Authors: Schmidt S, Linge A, Großer M, Lohaus F, Gudziol V, Nowak A, Tinhofer I, Budach V, Sak A, Stuschke M, Balermpas P, Rödel C, Schäfer H, Grosu AL, Abdollahi A, Debus J, Ganswindt U, Belka C, Pigorsch S, Combs SE, Mönnich D, Zips D, Baretton GB, Buchholz F, Baumann M, Krause M, Löck S, DKTK-ROG

Abstract
In this manuscript we compare the expression and applicability of biomarkers, from single genes and gene signatures, identified in patients with locally advanced head and neck squamous cell carcinoma (HNSCC) using the GeneChip Human Transcriptome Array 2.0, nCounter and real-time polymerase chain reaction (RT-PCR) analyses. Two multicentre retrospective HNSCC patient cohorts of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG), who received postoperative radiochemotherapy (PORT-C) or primary radiochemotherapy (primary RCTx) were considered. RT-PCR was performed for a limited number of 38 genes of the PORT-C cohort only. Correlations between the methods were evaluated by the Spearman rank correlation coefficient ρ. Patients were stratified based on the expression of putative cancer stem cell markers, hypoxia-associated gene signatures and a previously developed 7-gene signature. Loco-regional tumour control (LRC) was compared between these patient subgroups using log-rank tests. Gene expressions obtained from nCounter analyses were moderately correlated to GeneChip analyses (median ρ≈0.68). A higher correlation was obtained between nCounter analyses and RT-PCR (median ρ=0.84). Significant associations to LRC were observed for most of the considered biomarkers evaluated by both GeneChip and nCounter analyses. In general, all applied biomarkers (single genes and gene signatures) classified about 70% to 85% of the patients similarly. Overall, gene signatures seem to be more robust and showed a better transferability between different measurement methods.

PMID: 32247864 [PubMed - as supplied by publisher]

Alzheimer's disease beyond amyloid: can the repetitive failures of amyloid-targeted therapeutics inform future approaches to dementia drug discovery?

Biochem Pharmacol. 2020 Apr 02;:113945

Authors: Mullane K, Williams M

Abstract
Alzheimer's Disease (AD) therapeutics based on the amyloid hypothesis have repeatedly failed in clinical trials. Together with numerous reports that amyloid is present in brains from aged individuals without cognitive dysfunction, this suggests that the association of amyloid with AD is collateral rather than causal. The preeminence of the amyloid hypothesis has resulted in the 'systematic …thwart[ing of] alternative approaches' to AD/dementia driven by a 'cabal' of amyloid acolytes who have effectively controlled the ideas funded and published, which startups received venture investment and which programs were advanced in biopharmaceutical companies where they consulted. As a result, dementia research is estimated to be 15-30 years behind where it could be with conflicting data ignored in favor of the amyloid dogma and clinical trial failures being ascribed to faulty design or inadequacies in the compound selection process including flawed animal models. Major concerns regarding the precise diagnosis of AD/dementia and conflicting views on the validated status of fluid biomarker assays have resulted in trials that included patients with unknown amyloid pathologies. With the failure of the amyloid approach, emerging data on the role(s) of vascular, mitochondrial and synaptic network dysfunction, infection, diabetes, sleep, hearing loss, the gut microbiome and neuroinflammation/ innate immune function as dementia targets are driving research in new directions bolstered by recent findings on the genetic, omics and systems biology associated with AD/dementia. In moving forward, lessons learnt from the amyloid debacle should be used to enhance the objective identification of AD/dementia therapeutics using a multifactorial disease syndrome.

PMID: 32247851 [PubMed - as supplied by publisher]

Preface: Life through death-Key role of cellular suicide for colonial and organismal homeostasis.

Int Rev Cell Mol Biol. 2020;351:xi-xv

Authors: Spetz J, Galluzzi L

PMID: 32247583 [PubMed - as supplied by publisher]

TRAIL receptor signaling: From the basics of canonical signal transduction toward its entanglement with ER stress and the unfolded protein response.

Int Rev Cell Mol Biol. 2020;351:57-99

Authors: Stöhr D, Jeltsch A, Rehm M

Abstract
The cytokine tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is a member of the large TNF superfamily that can trigger apoptosis in transformed or infected cells by binding and activating two receptors, TRAIL receptor 1 (TRAILR1) and TRAIL receptor 2 (TRAILR2). Compared to other death ligands of the same family, TRAIL induces apoptosis preferentially in malignant cells while sparing normal tissue and has therefore been extensively investigated for its suitability as an anti-cancer agent. Recently, it was noticed that TRAIL receptor signaling is also linked to endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). The role of TRAIL receptors in regulating cellular apoptosis susceptibility therefore is broader than previously thought. Here, we provide an overview of TRAIL-induced signaling, covering the core signal transduction during extrinsic apoptosis as well as its link to alternative outcomes, such as necroptosis or NF-κB activation. We discuss how environmental factors, transcriptional regulators, and genetic or epigenetic alterations regulate TRAIL receptors and thus alter cellular TRAIL susceptibility. Finally, we provide insight into the role of TRAIL receptors in signaling scenarios that engage the unfolded protein response and discuss how these findings might be translated into new combination therapies for cancer treatment.

PMID: 32247582 [PubMed - as supplied by publisher]

12 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 2020/04/05

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.

12 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 2020/04/05

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.

20 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 2020/04/04

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.

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 2020/04/03

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.

22 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 2020/04/02

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.

36 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 2020/04/01

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.

52 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 2020/03/31

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.

52 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 2020/03/31

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.

The Impact of Sarcopenia and Low Muscle Attenuation on Overall Survival in Epithelial Ovarian Cancer: A Systematic Review and Meta-analysis.

Ann Surg Oncol. 2020 Mar 27;:

Authors: McSharry V, Mullee A, McCann L, Rogers AC, McKiernan M, Brennan DJ

Abstract
BACKGROUND: Sarcopenia is defined as a progressive loss of skeletal muscle mass, strength and physical performance. Myosteatosis is an increase of intra- and intermuscular fat and can be measured radiologically by muscle attenuation. The study aim was to perform a systematic review and meta-analysis on the prognostic potential of sarcopenia and low muscle attenuation in relation to 3-year survival rates (3YSR) and 5YSR in epithelial ovarian cancer (EOC).
METHODS: A systematic literature search was conducted using the databases Ovid Medline, EMBASE, and Scopus, using PRISMA guidelines, from inception to 10th of May 2019. Studies evaluated the prognostic potential of sarcopenia and low muscle attenuation on 3YSR and 5YSR in EOC. Quality assessment of included studies was performed using the Methodological Index for Non-Randomised Studies criteria.
RESULTS: A comprehensive search of databases resulted in the identification of 2194 studies, resulting in 1695 citations meeting the inclusion criteria. Six studies were included for systematic review. Sarcopenia was not significantly associated with improved 3YSR (OR 1.7, 95% CI 0.8-3.5, p = 0.15) or 5YSR (OR 1.8, 95% CI 1.0-3.2, p = 0.07) in meta-analysis. Normal muscle attenuation was associated with a favourable 3YSR (OR 3.0, 95% CI 2.0-4.5, p < 0.001) and 5YSR (OR 2.3, 95% CI 1.6-3.4, p < 0.001) compared to low muscle attenuation.
CONCLUSION: Our meta-analysis indicated normal muscle attenuation was significantly associated with improved 3YSR and 5YSR in patients with EOC. Sarcopenia was not significantly associated with 3YSR or 5YSR in patients with EOC.

PMID: 32221737 [PubMed - as supplied by publisher]

QuartataWeb: integrated chemical-protein-pathway mapping for polypharmacology and chemogenomics.

Bioinformatics. 2020 Mar 28;:

Authors: Li H, Pei F, Taylor DL, Bahar I

Abstract
SUMMARY: QuartataWeb is a user-friendly server developed for polypharmacological and chemogenomics analyses. Users can easily obtain information on experimentally verified (known) and computationally predicted (new) interactions between 5,494 drugs and 2,807 human proteins in DrugBank, and between 315,514 chemicals and 9,457 human proteins in the STITCH database. In addition, QuartataWeb links targets to KEGG pathways and GO annotations, completing the bridge from drugs/chemicals to function via protein targets and cellular pathways. It allows users to query a series of chemicals, drug combinations, or multiple targets, to enable multi-drug, multi-target, multi-pathway analyses, toward facilitating the design of polypharmacological treatments for complex diseases.
AVAILABILITY AND IMPLEMENTATION: QuartataWeb is freely accessible at http://quartata.csb.pitt.edu.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID: 32221612 [PubMed - as supplied by publisher]

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples.

Sci Rep. 2020 Mar 27;10(1):5630

Authors: Uellendahl-Werth F, Wolfien M, Franke A, Wolkenhauer O, Ellinghaus D

Abstract
RNA-Sequencing (RNA-Seq) of peripheral blood can be a valuable source of information for investigating the status and mechanism of diseases. However, blood contains 50-80% unwanted hemoglobin (Hb) transcripts. Lexogen's QuantSeq mRNA-Seq-Kit for Illumina RNA-Seq features a 'Globin Block' (GB) module that depletes Hb cDNAs during library preparation. Here, we aimed to assess GB's effectiveness and checked for technical biases attributable to GB. Using whole blood total RNA samples of 91 healthy individuals, we sequenced 91 pairs of GB and non-blocked samples (noGB) on Illumina HiSeq2500 and 8 pairs of GB/noGB technical replicates on HiSeq4000. GB reduced the fraction of Hb transcripts from 43% (s.d. 14%) to 8.0% (s.d. 4.3%). From GB samples we detected 1,397 more expressed genes at approximately 11 million reads per RNA-isolate. Enrichment and differential expression analyses did not reveal significant differences for GB and noGB samples with respect to molecular function. In contrast to results from studies that have examined the performance of GB during RNA isolation, we were able to assign GB to corresponding noGB samples (from multiple sequencing runs on HiSeq2500) with at least 89.8% accuracy from the complete correlation matrix of all GB/GB, noGB/noGB and GB/noGB pairs. However, the use of different sequencers (HiSeq2500 vs HiSeq4000) impaired assignment of technical replicates, whereas assignment of GB to corresponding noGB samples worked perfectly when sequencing on one lane on HiSeq4000. Lexogen's GB RNA-Seq module is a valuable addition during mRNA-Seq library preparation which works even with low amounts of input total RNA (50 ng per sample). GB facilitated the detection of low abundant transcripts and yielded more non-hemoglobin reads, while preserving biological information. We observed that differences in sequencing run and platform have a far greater effect on technical variation than the use of GB.

PMID: 32221409 [PubMed - as supplied by publisher]