Automated Classification for Pathological Prostate Images using AdaBoost-based

We present an AdaBoost-based Ensemble Learning for supporting automated Gleason grading of prostate adenocarcinoma (PRCA). The method is able to differentiate Gleason patterns 4–5 from patterns 1–3 as the patterns 4-5 are correlated to more aggressive disease while patterns 1-3 tend to reflect more favorable patient outcome. This method is based on various feature descriptors and classifiers for multiple color channels, including color channels of red, green and blue, as well as the optical intensity of hematoxylin and eosin stainings.

type: 
Conference Paper/Poster
journal: 
2016 IEEE Sympsosium Series on Computational Intelligence (IEEE SSCI 2016) Dec 6 to 9, Athens, Greece,

Development of Cell-Permeable, Non-Helical, Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer

There is a lack of current treatment options for ovarian clear cell carcinoma (CCC) and the cancer is often resistant to platinum-based chemotherapy. Hence there is an urgent need for novel therapeutics. The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in CCC and is seen as an attractive therapeutic target. This was validated through shRNA-mediated knockdown of the target protein, HNF1β, in five high- and low-HNF1β-expressing CCC lines.

type: 
Journal Paper
journal: 
Angewandte Chemie, Vol. 56, Issue 2, Jan 9, 2017 Pg 524-529, doi: 10.1002/anie.201609427
pubmed: 
27918136
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27918136
Impact Factor: 
11.709

Towards allosterically increased catalytic activity of insulin degrading enzyme (IDE) against amyloid peptides

Physiological role of insulin degrading enzyme (IDE) in the intracytosolic clearance of amyloid beta (Aβ) and other amyloid-like peptides supports a hypothesis that human IDE hyperactivation could be therapeutically beneficial in the treatment of the late onset Alzhimer’s disease (AD). The major challenge towards this goal is to increase specific catalytic activity of IDE against the Aβ-substrate.

type: 
Journal Paper
journal: 
Biochemistry 2016, doi: 10.1021/acs.biochem.6b00783
Url: 
http://pubs.acs.org/doi/abs/10.1021/acs.biochem.6b00783
Impact Factor: 
2.87

Palmitoylation of caspase-6 by HIP14 regulates its activation

Caspase-6 (CASP6) has an important role in axonal degeneration during neuronal apoptosis and in the neurodegenerative diseases Alzheimer and Huntington disease. Decreasing CASP6 activity may help to restore neuronal function in these and other diseases such as stroke and ischemia, where increased CASP6 activity has been implicated. The key to finding approaches to decrease CASP6 activity is a deeper understanding of the mechanisms regulating CASP6 activation.

type: 
Journal Paper
journal: 
Cell Death and Differentiation (2016), 1-12, doi: doi:10.1038/cdd.2016.139
pubmed: 
27911442
Url: 
https://www.ncbi.nlm.nih.gov/pubmed/27911442
Impact Factor: 
8.218

Water-Bridge Mediates Recognition of mRNA Cap in eIF4E

Ligand binding pockets in proteins contain water molecules, which play important roles in modulating protein-ligand interactions. Available crystallographic data for the 5′ mRNA cap-binding pocket of the translation initiation factor protein eIF4E shows several structurally conserved waters, which also persist in molecular dynamics simulations. These waters engage an intricate hydrogen-bond network between the cap and protein.

type: 
Journal Paper
journal: 
Structure 25, 1–7, January 3, 2017
Url: 
http://www.cell.com/structure/fulltext/S0969-2126(16)30346-X
Impact Factor: 
5.237
Date of acceptance: 
2016-11-07

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

BACKGROUND:
While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.

RESULTS:

type: 
Journal Paper
journal: 
Biology Direct 2016, 11:63, DOI: 10.1186/s13062-016-0163-0
pubmed: 
27894340
Url: 
https://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0163-0
Impact Factor: 
3.016
Date of acceptance: 
2016-10-24

R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes.

type: 
Journal Paper
journal: 
Nucleic Acids Research, 2016, 1, doi: 10.1093/nar/gkw1054
Url: 
https://academic.oup.com/nar/article/45/D1/D119/2605726/R-loopDB-a-database-for-R-loop-forming-sequences
Impact Factor: 
9.202
Date of acceptance: 
2016-10-20

Transition steps in peroxide reduction and a molecular switch for peroxide robustness of prokaryotic peroxiredoxins

In addition to their antioxidant function, the eukaryotic peroxiredoxins (Prxs) facilitate peroxide-mediated signaling by undergoing controlled inactivation by peroxide-driven over-oxidation. In general, the bacterial enzyme lacks this controlled inactivation mechanism, making it more resistant to high H2O2 concentrations. During peroxide reduction, the active site alternates between reduced, fully folded (FF), and oxidized, locally unfolded (LU) conformations.

type: 
Journal Paper
journal: 
Scientific Reports 6, 2016, doi: 10.1038/srep37610
Url: 
http://www.nature.com/articles/srep37610
Impact Factor: 
5.228
Date of acceptance: 
2016-10-31

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment

The envelope of Gram-negative bacteria is highly complex, containing separate outer and inner membranes and an intervening periplasmic space encompassing a peptidoglycan (PGN) cell wall. The PGN scaffold is anchored non-covalently to the outer membrane via globular OmpA-like domains of various proteins. We report atomically detailed simulations of PGN bound to OmpA in three different states, including the isolated C-terminal domain (CTD), the full-length monomer, or the complete full-length dimeric form.

type: 
Journal Paper
journal: 
Structure 2016, Vol. 24, Issue 12, 6 Dec 2016, Pg 2227-2235, doi: 10.1016/j.str.2016.10.009
pubmed: 
27866852
Url: 
http://www.cell.com/structure/abstract/S0969-2126(16)30317-3
Impact Factor: 
5.237
Date of acceptance: 
2016-10-14

Protein function machinery: from basic structural units to modulation of activity

Contemporary protein structure is a result of the trade off between the laws of physics and the evolutionary selection. The polymer nature of proteins played a decisive role in establishing the basic structural and functional units of soluble proteins. We discuss how these elementary building blocks work in the hierarchy of protein domain structure, co-translational folding, as well as in enzymatic activity and molecular interactions.

type: 
Journal Paper
journal: 
Current Opinion in Structural Biology, Vol. 42, Feb 17, Pg 67-74, doi: 10.1016/j.sbi.2016.10.021
pubmed: 
27865209
Url: 
http://www.sciencedirect.com/science/article/pii/S0959440X1630183X
Impact Factor: 
6.7
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