SVD-clustering, a general image-analyzing method explained and demonstrated on model and Raman micro-spectroscopic maps

An image analyzing method (SVD-clustering) is presented. Amplitude vectors of SVD factorization (V1…Vi) were introduced into the imaging of the distribution of the corresponding Ui basis-spectra. Since each Vi vector contains each point of the map, plotting them along the X, Y, Z dimensions of the map reconstructs the spatial distribution of the corresponding Ui basis-spectrum. This gives valuable information about the first, second, etc. higher-order deviations present in the map. We extended SVD with a clustering method, using the significant Vi vectors from the VT matrix as coordinates of image points in a ne-dimensional space (ne is the effective rank of the data matrix). This way every image point had a corresponding coordinate in the ne-dimensional space and formed a point set. Clustering was applied to this point set. SVD-clustering is universal; it is applicable to any measurement where data are recorded as a function of an external parameter (time, space, temperature, concentration, species, etc.). Consequently, our method is not restricted to spectral imaging, it can find application in many different 2D and 3D image analyses. Using SVD-clustering, we have shown on models the theoretical possibilities and limitations of the method, especially in the context of creating, meaning/interpreting of cluster spectra. Then for real-world samples, two examples are presented, where we were able to reveal minute alterations in the samples (changing cation ratios in minerals, differently structured cellulose domains in plant root) with spatial resolution. © 2020, The Author(s)

The unacknowledged legacy

This paper presents a critical discussion of the treatment of mimetic art, and particularly poetry and the theatre, in the work of the Athenian philosopher Plato (427-347 BC). It centres on Plato's discussion of the corrupting powers of the arts in the Republic, and the implications that his fierce attack on poetry and theatre have for his construction of the ideal polity. The legacy of Platonic ideas in later elaborations of the corrupting power of the arts is discussed. Furthermore, the paper investigates the relationship between current debates on cultural policy and the Platonic idea that the transformative powers of the arts ought to be harnessed by the state to promote a just society. The conclusion thus reached is that “instrumental cultural policy”, rather then being a modern invention, was in fact first theorized precisely in Plato's Republic

The CCP4 suite: integrative software for macromolecular crystallography

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.Jon Agirre is a Royal Society University Research Fellow (UF160039 and URF\R\221006). Mihaela Atanasova is funded by the UK Engineering and Physical Sciences Research Council (EPSRC; EP/R513386/1). Haroldas Bagdonas is funded by The Royal Society (RGF/R1/181006). Jose´ Javier Burgos-Ma´rmol and Daniel J. Rigden are supported by the BBSRC (BB/S007105/1). Robbie P. Joosten is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 871037 (iNEXTDiscovery) and by CCP4. This work was supported by the Medical Research Council as part of United Kingdom Research and Innovation, also known as UK Research and Innovation: MRC file reference No. MC_UP_A025_1012 to Garib N. Murshudov, which also funded Keitaro Yamashita, Paul Emsley and Fei Long. Robert A. Nicholls is funded by the BBSRC (BB/S007083/1). Soon Wen Hoh is funded by the BBSRC (BB/T012935/1). Kevin D. Cowtan and Paul S. Bond are funded in part by the BBSRC (BB/S005099/1). John Berrisford and Sameer Velankar thank the European Molecular Biology Laboratory–European Bioinformatics Institute, who supported this work. Andrea Thorn was supported in the development of AUSPEX by the German Federal Ministry of Education and Research (05K19WWA and 05K22GU5) and by Deutsche Forschungsgemeinschaft (TH2135/2-1). Petr Kolenko and Martin Maly´ are funded by the MEYS CR (CZ.02.1.01/0.0/0.0/16_019/0000778). Martin Maly´ is funded by the Czech Academy of Sciences (86652036) and CCP4/STFC (521862101). Anastassis Perrakis acknowledges funding from iNEXT (grant No. 653706), iNEXT-Discovery (grant No. 871037), West-Life (grant No. 675858) and EOSC-Life (grant No. 824087) funded by the Horizon 2020 program of the European Commission. Robbie P. Joosten has been the recipient of a Veni grant (722.011.011) and a Vidi grant (723.013.003) from the Netherlands Organization for Scientific Research (NWO). Maarten L. Hekkelman, Robbie P. Joosten and Anastassis Perrakis thank the Research High Performance Computing facility of the Netherlands Cancer Institute for providing and maintaining computation resources and acknowledge the institutional grant from the Dutch Cancer Society and the Dutch Ministry of Health, Welfare and Sport. Tarik R. Drevon is funded by the BBSRC (BB/S007040/1). Randy J. Read is supported by a Principal Research Fellowship from the Wellcome Trust (grant 209407/Z/17/Z). Atlanta G. Cook is supported by a Wellcome Trust SRF (200898) and a Wellcome Centre for Cell Biology core grant (203149). Isabel Uso´n acknowledges support from STFC-UK/CCP4: ‘Agreement for the integration of methods into the CCP4 software distribution, ARCIMBOLDO_LOW’ and Spanish MICINN/AEI/FEDER/UE (PID2021-128751NB-I00). Pavol Skubak and Navraj Pannu were funded by the NWO Applied Sciences and Engineering Domain and CCP4 (grant Nos. 13337 and 16219). Bernhard Lohkamp was supported by the Ro¨ntgen A˚ ngstro¨m Cluster (grant 349-2013-597). Nicholas Pearce is currently funded by the SciLifeLab and Wallenberg Data Driven Life Science Program (grant KAW 2020.0239) and has previously been funded by a Veni Fellowship (VI.Veni.192.143) from the Dutch Research Council (NWO), a Long-term EMBO fellowship (ALTF 609-2017) and EPSRC grant EP/G037280/1. David M. Lawson received funding from BBSRC Institute Strategic Programme Grants (BB/P012523/1 and BB/P012574/1). Lucrezia Catapano is the recipient of an STFC/CCP4-funded PhD studentship (Agreement No: 7920 S2 2020 007).Peer reviewe

Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): A rigid molecular scaffold

The Ecballium elaterium trypsin inhibitor II (EETI-II) belongs to the family of squash inhibitors and is one of the strongest inhibitors known for trypsin. The eight independent molecules of EETI-II in the crystal structure reported here provide a good opportunity to test the hypothesis that this small cystine-knot protein (knottin) is sufficiently rigid to be used as a molecular scaffold for protein-engineering purposes. To extend this test, the structures of two complexes of EETI-II with trypsin have also been determined, one carrying a four-amino-acid mutation of EETI-II. The remarkable similarity of these structures confirms the rigidity of the molecular framework and hence its suitability as a molecular scaffold. © 2005 International Union of Crystallography - all rights reserved.This work was supported by the Deutsche Forschungsgemeinschaft (SFB416) and by the Fonds der Chemischen Industrie. IU thanks the Spanish MEC for grant BIO2003-06653Peer Reviewe