32 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 2019/10/02

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.

76 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 2019/10/01

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.

Perinatal high-fat diet impairs pup retrieval and induces sex-specific changes in ultrasonic vocalization characteristics of rat pups.

Dev Psychobiol. 2019 Sep 28;:

Authors: Abuaish S, Tse EK, McGowan PO

Abstract
Rodent pups emit ultrasonic vocalizations (USVs) to solicit maternal behavior, promoting their survival. Conversely, maternal behaviors affect the expression of pup USVs. We previously demonstrated that a maternal diet high in saturated fat (HFD) alters maternal behavior and is associated with early maturation of pups and their stress physiology. Here, we assessed the developmental profiles of pup USVs using quantitative and qualitative measures on postnatal days (PND)7 and 13. Quantitative measures included call counts, duration, and frequency, while qualitative measures examined calls' sonographic structures. HFD offspring lacked the typical decrease in USV numbers with age observed among control offspring. They also had shorter calls at PND7 compared to control and HFD offspring at PND13. HFD female offspring showed a greater number of one-frequency-sweep calls, while male pups showed a greater number of two-frequency-sweep calls compared to control offspring. Concomitantly, HFD dams showed impaired pup retrieval on PND7. The data suggest that fewer USVs of shorter duration in HFD offspring may alter dam solicitation and thus impair maternal pup retrieval. This study highlights the impacts of perinatal HFD exposure on the dyadic reciprocal interaction between dam and pups, which may set the stage for long-lasting effects on offspring physiology and behavior.

PMID: 31564067 [PubMed - as supplied by publisher]

Plants are intelligent, here's how.

Ann Bot. 2019 Sep 29;:

Authors: Calvo P, Gagliano M, Souza GM, Trewavas A

Abstract
HYPOTHESES: The drive to survive is a biological universal. Intelligent behaviour is usually recognised when individual organisms including plants, in the face of fiercely competitive or adverse, real world circumstances, change their behaviour to improve their probability of survival.
SCOPE: This article explains the potential relationship of intelligence to adaptability and emphasises the need for recognising individual variation in intelligence showing it to be goal directed and thus being purposeful. Intelligent behaviour in single cells and microbes is frequently reported. Individual variation might be underpinned by a novel learning mechanism described in detail. The requirements for real world circumstances are outlined, the relationship to organic selection indicated together with niche construction as a good example of intentional behaviour that should improve survival. Adaptability is important in crop development but the term may be complex incorporating numerous behavioural traits some of which are indicated.
CONCLUSION: There is real biological benefit to regarding plants as intelligent both from a fundamental issue of understanding plant life but also from providing a direction for fundamental future research and in crop breeding.

PMID: 31563953 [PubMed - as supplied by publisher]

Adenoviral Infections in Singapore: Should New Antiviral Therapies and Vaccines Be Adopted?

J Infect Dis. 2019 Sep 30;:

Authors: Coleman KK, Wong CC, Jayakumar J, Nguyen TT, Wong AWL, Yadana S, Thoon KC, Chan KP, Low JG, Kalimuddin S, Dehghan S, Kang J, Shamsaddini A, Seto D, Su YCF, Gray GC

Abstract
BACKGROUND: A number of serious human adenovirus (HAdV) outbreaks have been recently reported: HAdV-B7 (Israel, Singapore, and USA), HAdV-B7d (USA and China), HAdV-D8, -D54, and -C2 (Japan), HAdV-B14p1 (USA, Europe, and China), and HAdV-B55 (China, Singapore, and France).
METHODS: To understand the epidemiology of HAdV infections in Singapore, we studied 533 HAdV-positive clinical samples collected from 396 pediatric and 137 adult patients in Singapore from 2012-2018. Genome sequencing and phylogenetic analyses were performed to identify HAdV genotypes, clonal clusters and recombinant or novel HAdVs.
RESULTS: The most prevalent genotypes identified were HAdV-B3 (35.6%), HAdV-B7 (15.4%) and HAdV-E4 (15.2%). We detected four new HAdV-C strains and detected incursions with HAdV-B7 (odds ratio [OR], 14.6 [95% CI, 4.1-52.0]) and HAdV-E4 (OR, 13.6 [3.9-46.7]) among pediatric patients over time. Additionally, immunocompromised patients (adjusted OR [aOR], 11.4 [3.8-34.8]) and patients infected with HAdV-C2 (aOR, 8.5 [1.5-48.0]), HAdV-B7 (aOR, 3.7 [1.2-10.9]), or HAdV-E4 (aOR, 3.2 [1.1-8.9]) were at increased risk for severe disease.
CONCLUSION: Singapore would benefit from more frequent studies of clinical HAdV genotypes to identify patients at risk for severe disease and help guide the use of new antiviral therapies, such as brincidofovir, and potential administration of human adenovirus 4 and 7 vaccine.

PMID: 31563943 [PubMed - as supplied by publisher]

A Consensus Molecular Classification of Muscle-invasive Bladder Cancer.

Eur Urol. 2019 Sep 25;:

Authors: Kamoun A, Reyniès A, Allory Y, Sjödahl G, Gordon Robertson A, Seiler R, Hoadley KA, Groeneveld CS, Al-Ahmadie H, Choi W, Castro MAA, Fontugne J, Eriksson P, Mo Q, Kardos J, Zlotta A, Hartmann A, Dinney CP, Bellmunt J, Powles T, Malats N, Chan KS, Kim WY, McConkey DJ, Black PC, Dyrskjøt L, Höglund M, Lerner SP, Real FX, Radvanyi F, Bladder Cancer Molecular Taxonomy Group

Abstract
BACKGROUND: Muscle-invasive bladder cancer (MIBC) is a molecularly diverse disease with heterogeneous clinical outcomes. Several molecular classifications have been proposed, but the diversity of their subtype sets impedes their clinical application.
OBJECTIVE: To achieve an international consensus on MIBC molecular subtypes that reconciles the published classification schemes.
DESIGN, SETTING, AND PARTICIPANTS: We used 1750 MIBC transcriptomic profiles from 16 published datasets and two additional cohorts.
OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We performed a network-based analysis of six independent MIBC classification systems to identify a consensus set of molecular classes. Association with survival was assessed using multivariable Cox models.
RESULTS AND LIMITATIONS: We report the results of an international effort to reach a consensus on MIBC molecular subtypes. We identified a consensus set of six molecular classes: luminal papillary (24%), luminal nonspecified (8%), luminal unstable (15%), stroma-rich (15%), basal/squamous (35%), and neuroendocrine-like (3%). These consensus classes differ regarding underlying oncogenic mechanisms, infiltration by immune and stromal cells, and histological and clinical characteristics, including outcomes. We provide a single-sample classifier that assigns a consensus class label to a tumor sample's transcriptome. Limitations of the work are retrospective clinical data collection and a lack of complete information regarding patient treatment.
CONCLUSIONS: This consensus system offers a robust framework that will enable testing and validation of predictive biomarkers in future prospective clinical trials.
PATIENT SUMMARY: Bladder cancers are heterogeneous at the molecular level, and scientists have proposed several classifications into sets of molecular classes. While these classifications may be useful to stratify patients for prognosis or response to treatment, a consensus classification would facilitate the clinical use of molecular classes. Conducted by multidisciplinary expert teams in the field, this study proposes such a consensus and provides a tool for applying the consensus classification in the clinical setting.

PMID: 31563503 [PubMed - as supplied by publisher]

Approximate Bayesian Computation for infectious disease modelling.

Epidemics. 2019 Sep 25;:100368

Authors: Minter A, Retkute R

Abstract
Approximate Bayesian Computation (ABC) techniques are a suite of model fitting methods which can be implemented without a using likelihood function. In order to use ABC in a time-efficient manner users must make several design decisions including how to code the ABC algorithm and the type of ABC algorithm to use. Furthermore, ABC relies on a number of user defined choices which can greatly effect the accuracy of estimation. Having a clear understanding of these factors in reducing computation time and improving accuracy allows users to make more informed decisions when planning analyses. In this paper, we present an introduction to ABC with a focus of application to infectious disease models. We present a tutorial on coding practice for ABC in R and three case studies to illustrate the application of ABC to infectious disease models.

PMID: 31563466 [PubMed - as supplied by publisher]

Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes.

Mol Cell. 2019 Sep 19;:

Authors: Zamudio AV, Dall'Agnese A, Henninger JE, Manteiga JC, Afeyan LK, Hannett NM, Coffey EL, Li CH, Oksuz O, Sabari BR, Boija A, Klein IA, Hawken SW, Spille JH, Decker TM, Cisse II, Abraham BJ, Lee TI, Taatjes DJ, Schuijers J, Young RA

Abstract
The gene expression programs that define the identity of each cell are controlled by master transcription factors (TFs) that bind cell-type-specific enhancers, as well as signaling factors, which bring extracellular stimuli to these enhancers. Recent studies have revealed that master TFs form phase-separated condensates with the Mediator coactivator at super-enhancers. Here, we present evidence that signaling factors for the WNT, TGF-β, and JAK/STAT pathways use their intrinsically disordered regions (IDRs) to enter and concentrate in Mediator condensates at super-enhancers. We show that the WNT coactivator β-catenin interacts both with components of condensates and DNA-binding factors to selectively occupy super-enhancer-associated genes. We propose that the cell-type specificity of the response to signaling is mediated in part by the IDRs of the signaling factors, which cause these factors to partition into condensates established by the master TFs and Mediator at genes with prominent roles in cell identity.

PMID: 31563432 [PubMed - as supplied by publisher]

40 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 2019/09/29

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.

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 2019/09/28

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.

21 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 2019/09/27

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 2019/09/27

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.

44 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 2019/09/26

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.

39 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 2019/09/26

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 2019/09/25

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.

26 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 2019/09/24

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.

Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma.

Gut. 2019 Sep 21;:

Authors: Ooi WF, Nargund AM, Lim KJ, Zhang S, Xing M, Mandoli A, Lim JQ, Ho SWT, Guo Y, Yao X, Lin SJ, Nandi T, Xu C, Ong X, Lee M, Tan AL, Lam YN, Teo JX, Kaneda A, White KP, Lim WK, Rozen SG, Teh BT, Li S, Skanderup AJ, Tan P

Abstract
OBJECTIVE: Genomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS).
DESIGN: We applied PeNChIP-seq to 11 primary GCs and matched normal tissues combined with WGS profiles of >200 GCs. Epigenome profiles were analysed alongside matched RNA-seq data to identify tumour-associated enhancer-based SVs with altered cancer transcription. Functional validation of candidate enhancer-based SVs was performed using CRISPR/Cas9 genome editing, chromosome conformation capture assays (4C-seq, Capture-C) and Hi-C analysis of primary GCs.
RESULTS: PeNChIP-seq/WGS revealed ~150 enhancer-based SVs in GC. The majority (63%) of SVs linked to target gene deregulation were associated with increased tumour expression. Enhancer-based SVs targeting CCNE1, a key driver of therapy resistance, occurred in 8% of patients frequently juxtaposing diverse distal enhancers to CCNE1 proximal regions. CCNE1-rearranged GCs were associated with high CCNE1 expression, disrupted CCNE1 topologically associating domain (TAD) boundaries, and novel TAD interactions in CCNE1-rearranged primary tumours. We also observed IGF2 enhancer-based SVs, previously noted in colorectal cancer, highlighting a common non-coding genetic driver alteration in gastric and colorectal malignancies.
CONCLUSION: Integrated paired-end NanoChIP-seq and WGS of gastric tumours reveals tumour-associated regulatory SV in regions associated with both simple and complex genomic rearrangements. Genomic rearrangements may thus exploit enhancer-hijacking as a common mechanism to drive oncogene expression in GC.

PMID: 31542774 [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 2019/09/22

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.

17 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 2019/09/21

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.

17 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 2019/09/21

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.