Commentary: Augmented Reality Scientific Phone Apps - making the APD AR Holistic Review app and using existing AR apps for scientific publications

Published date : 02 Oct 2018

The average scientific publication is not the most palatable of reading materials, especially to those not in the relevant disciplines. Yet, conveying scientific concepts easily is precisely what scientific publications are meant to do. Imagine what the use of video pictures/paintings as depicted in the Harry Potter movie series can do to make things easier! While the fantasy of moving photos/pictures does not exist physically in the real world, just as Santa Claus cannot travel the world today without being shot down by anti-missiles, there are some shadows of reality in this idea.

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Journal Paper
journal
Scientific Phone Apps and Mobile Devices (2018) 4:4, doi:10.30943/2018/28092018

Editorial : A New Home for "Scientific Phone Apps and Mobile Devices" Journal

Published date : 28 Sep 2018

The original intent of academic publication to disseminate information and findings to the community for scientific progress has taken different twists and turns particularly in the last few decades. With the Internet, there is now the option of E-publications, and more recently, open access publishing to make articles freely available to readers. No longer are the articles restricted to subscribing academics, but now also to the general public.

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Journal Paper
journal
Scientific Phone Apps and Mobile Devices (2018) 4:3, doi: 10.30943/2018/26042018

Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000

Published date : 28 Sep 2018

The mentioning of gene names in the body of the scientific literature 1901-2017 and their fractional counting was used as a proxy to assess the level of biological function discovery. We define a literature score of one as full publication equivalent (FPE), the amount of literature necessary to achieve one publication solely dedicated to a gene. We find that less than 5000 human genes have each at least 100 FPEs in the available literature corpus.

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Journal Paper
journal
Proteomics 2018, Sep 28, doi: 10.1002/pmic.201800093
Impact Factor
3.532

Molecular mechanism of the Escherichia coli AhpC in the function of a chaperone under heat-shock conditions

Published date : 20 Sep 2018

Peroxiredoxins (Prxs) are ubiquitous antioxidants utilizing a reactive cysteine for peroxide reduction and acting as a molecular chaperone under various stress conditions. Besides other stimulating factors, oxidative- and heat stress conditions trigger their ATP-independent chaperoning function. So far, many studies were intended to reveal the chaperoning mechanisms of the so-called sensitive Prxs of eukaryotes, which are susceptible to inactivation by over-oxidation of its reactive cysteine during H2O2 reduction.

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Journal Paper
journal
Scientific Reports 8, No. 14151, 2018, doi: 10.1038/s41598-018-32527-7
Impact Factor
4.122

Single-molecule studies of flavivirus envelope dynamics: Experiment and computation

Published date : 14 Sep 2018

Flaviviruses are simple enveloped viruses exhibiting complex structural and functional heterogeneities. Decades of research have provided crucial basic insights, antiviral medication and moderately successful gene therapy trials. The most infectious particle is, however, not always the most abundant one in a population, questioning the utility of classic ensemble-averaging virology approaches. Indeed, viral replication is often not particularly efficient, prone to errors or containing parallel routes.

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Journal Paper
journal
Progress in Biophysics and Molecular Biology, 2018, Sep 14, doi: 10.1016/j.pbiomolbio.2018.09.001
Impact Factor
3.427

Identification of FDA-approved drugs as novel allosteric inhibitors of human executioner caspases

Published date : 14 Sep 2018

The regulation of apoptosis is a tightly-coordinated process and caspases are its chief regulators. Of special importance are the executioner caspases, caspase-3/7, the activation of which irreversibly sets the cell on the path of death. Dysregulation of apoptosis, particularly an increased rate of cell death lies at the root of numerous human diseases. Although several peptide-based inhibitors targeting the homologous active site region of caspases have been developed, owing to their non-specific activity and poor pharmacological properties their use has largely been restricted.

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Journal Paper
journal
Proteins: Structure, Function and Bioinformatics, 2018 Sep 8. doi: 10.1002/prot.25601
Impact Factor
2.274

Structures of the Human PGD2 Receptor CRTH2 Reveal Novel Mechanisms for Ligand Recognition

Published date : 13 Sep 2018

The signaling of prostaglandin D 2 (PGD 2) through G-protein-coupled receptor (GPCR) CRTH2 is a major pathway in type 2 inflammation. Compelling evidence suggests the therapeutic benefits of blocking CRTH2 signaling in many inflammatory disorders. Currently, a number of CRTH2 antagonists are under clinical investigation, and one compound, fevipiprant, has advanced to phase 3 clinical trials for asthma. Here, we present the crystal structures of human CRTH2 with two antagonists, fevipiprant and CAY10471.

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Journal Paper
journal
Molecular Cell, 2018, doi: 10.1016/j.molcel.2018.08.009
Impact Factor
14.428

Integrated Multimodal Evaluation of Genotoxicity in ZFN-Modified Primary Human Cells

Published date : 29 Aug 2018

Iatrogenic adverse events in clinical trials of retroviral vector-mediated gene-corrected cells have prioritized the urgent need for more comprehensive and stringent assessment of potentially genotoxic off-target alterations and the biosafety of cells intended for therapeutic applications. Genome editing tools such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced palindromic repeats (CRISPR)-Cas9 nuclease systems are being investigated as safer and efficient alternatives for site-directed genome modification.

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Book/Book Chapter
journal
Methods in Molecular Biology: Zinc Finger Proteins, 2018;1867:141-164. doi: 10.1007/978-1-4939-8799-3_11

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides

Published date : 17 Aug 2018

Thrombin-derived C-terminal peptides (TCPs) of about 2 kDa are present in wounds, where they exert anti-endotoxic functions. Employing a combination of nuclear magnetic resonance spectroscopy (NMR), biophysical, mass spectrometry and cellular studies combined with in silico multiscale modelling, we here determine the bound conformation of HVF18 (HVFRLKKWIQKVIDQFGE), a TCP generated by neutrophil elastase, in complex with bacterial lipopolysaccharide (LPS) and define a previously undisclosed interaction between TCPs and human CD14.

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Journal Paper
journal
Nature Communications, 2018 Jul 17;9(1):2762. doi: 10.1038/s41467-018-05242-0
Impact Factor
12.353

Conformational Transitions of Melittin between Aqueous and Lipid Phases: Comparison of Simulations with Experiments

Published date : 16 Aug 2018

Peptides are promising drug candidates with advantageous therapeutic properties. However, their inherent flexibility makes the development of structure−activity relationships difficult. Molecular dynamics simulations have been widely used to study peptide conformations, but they are limited by force field parameters.

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Journal Paper
journal
The Journal of Physical Chemistry B, 2018, doi: 10.1021/acs.jpcb.8b06781
Impact Factor
3.146