Machine-Learning Studies on Spin Models

Published date : 02 Apr 2020

With the recent developments in machine learning, Carrasquilla and Melko have proposed a paradigm that is complementary to the conventional approach for the study of spin models. As an alternative to investigating the thermal average of macroscopic physical quantities, they have used the spin configurations for the classification of the disordered and ordered phases of a phase transition through machine learning. We extend and generalize this method.

type
Journal Paper
journal
Scientific Reports 10, Article no. 2177, 2020, doi: 10.1038/s41598-020-58263-5
Impact Factor
4.011

Identification and engineering of 32 membered antifungal macrolactone notonesomycins

Published date : 02 Apr 2020

Notonesomycin A is a 32-membered bioactive glycosylated macrolactone known to be produced by Streptomyces aminophilus subsp. notonesogenes 647-AV1 and S. aminophilus DSM 40186. In a high throughput antifungal screening campaign, we identified an alternative notonesomycin A producing strain, Streptomyces sp. A793, and its biosynthetic gene cluster. From this strain, we further characterized a new more potent antifungal non-sulfated analogue, named notonesomycin B.

type
Journal Paper
journal
Microbial Cell Factories, 2020 Mar 19;19(1):71. doi: 10.1186/s12934-020-01328-x
Impact Factor
4.402

Multiscale modelling and simulation of viruses

Published date : 02 Apr 2020

In recent years, advances in structural biology, integrative modelling, and simulation approaches have allowed us to gain unprecedented insights into viral structure and dynamics. In this article we survey recent studies utilizing this wealth of structural information to build computational models of partial or complete viruses and to elucidate mechanisms of viral function.

type
Journal Paper
journal
Current Opinion in Structural Biology 2020, 61:146-152, doi: 10.1016/j.sbi.2019.12.019
Impact Factor
7.052

Automated grading of acne vulgaris by deep learning with convolutional neural networks

Published date : 26 Mar 2020

BACKGROUND:
The visual assessment and severity grading of acne vulgaris by physicians can be subjective, resulting in inter- and intra-observer variability.

OBJECTIVE:
To develop and validate an algorithm for the automated calculation of the Investigator's Global Assessment (IGA) scale, to standardize acne severity and outcome measurements.

type
Journal Paper
journal
Skin Research & Technology, Vol 26, Issue 2, March 2020, Pg 187-192, doi: 10.1111/srt.12794
Impact Factor
1.657

A common MET polymorphism harnesses HER2 signaling to drive aggressive squamous cell carcinoma

Published date : 25 Mar 2020

c-MET receptors are activated in cancers through genomic events like tyrosine kinase domain mutations, juxtamembrane splicing mutation and amplified copy numbers, which can be inhibited by c-MET small molecule inhibitors. Here, we discover that the most common polymorphism known to affect MET gene (N375S), involving the semaphorin domain, confers exquisite binding affinity for HER2 and enables METN375S to interact with HER2 in a ligand-independent fashion.

type
Journal Paper
journal
Nature Communication, 11, 1556 (2020), doi: 10.1038/s41467-020-15318-5
Impact Factor
11.878

Investigation of three clusters of COVID-19 in Singapore: implications for surveillance and response measures - Singapore 2019 Novel Coronavirus Outbreak Research Team

Published date : 16 Mar 2020

BACKGROUND:
Three clusters of coronavirus disease 2019 (COVID-19) linked to a tour group from China, a company conference, and a church were identified in Singapore in February, 2020.

type
Journal Paper
journal
Lancet 2020, Vol. 395, Issue 10229, Pg 1039-1046, March 28, 2020, doi: 10.1016/S0140-6736(20)30528-6
Impact Factor
59.2

Thrombin-derived C-terminal fragments aggregate and scavenge bacteria and their proinflammatory products.

Published date : 13 Mar 2020

Thrombin-derived C-terminal peptides (TCPs), including a major 11-kDa fragment (TCP96), are produced through cleavage by human neutrophil elastase and aggregate lipopolysaccharide (LPS) and the Gram-negative bacterium Escherichia coli However, the physiological roles of TCP96 in controlling bacterial infections and reducing LPS-induced inflammation are unclear.

type
Journal Paper
journal
Journal of Biological Chemistry, 2020 Mar 13;295(11):3417-3430. doi: 10.1074/jbc.RA120.012741
Impact Factor
3.075

The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance

Published date : 10 Mar 2020

The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic drugs. In addressing the crux of the issue, various attempts to estimate the mutation rate of HIV-1 resulted in a large range of 10−5–10−3 errors/bp/cycle due to the use of different types of investigation methods.

type
Journal Paper
journal
Viruses 2020, 12, 297; doi:10.3390/v12030297
Impact Factor
3.811

How ligand binding affects the dynamical transition temperature in proteins

Published date : 03 Mar 2020

The biochemical functions of proteins are activated at the protein glass transition temperature, which has been proposed to be dependent upon protein‐water interactions. However, at the molecular level it is unclear how ligand binding to well‐defined binding sites can influence this transition temperature. We thus report molecular dynamics (MD) simulations of the ϵ subunit from thermophilic Bacillus PS3 in the ATP‐free and ligand‐bound states over a range of temperatures from 20 to 300 K, to study the influence of ligand association upon the transition temperature.

type
Journal
journal
ChemPhysChem 2020, doi:10.1002/cphc.201901221
Impact Factor
3.075

Viruses go modular

Published date : 28 Feb 2020

The WW domain is a modular protein structure that recognizes the proline-rich Pro–Pro-x-Tyr (PPxY) motif contained in specific target proteins. The compact modular nature of the WW domain makes it ideal for mediating interactions between proteins in complex networks and signaling pathways of the cell (e.g. the Hippo pathway). As a result, WW domains play key roles in a plethora of both normal and disease processes.

type
Journal Paper
journal
Journal of Biological Chemistry, 2020, doi: 10.1074/jbc.REV119.012414
Impact Factor
4.106