archivist: An R Package for Managing, Recording and Restoring Data Analysis Results

Everything that exists in R is an object [Chambers2016]. This article examines what would be possible if we kept copies of all R objects that have ever been created. Not only objects but also their properties, meta-data, relations with other objects and information about context in which they were created. We introduce archivist, an R package designed to improve the management of results of data analysis. Key functionalities of this package include: (i) management of local and remote repositories which contain R objects and their meta-data (objects' properties and relations between them); (ii) archiving R objects to repositories; (iii) sharing and retrieving objects (and it's pedigree) by their unique hooks; (iv) searching for objects with specific properties or relations to other objects; (v) verification of object's identity and context of it's creation. The presented archivist package extends, in a combination with packages such as knitr and Sweave, the reproducible research paradigm by creating new ways to retrieve and validate previously calculated objects. These new features give a variety of opportunities such as: sharing R objects within reports or articles; adding hooks to R objects in table or figure captions; interactive exploration of object repositories; caching function calls with their results; retrieving object's pedigree (information about how the object was created); automated tracking of the performance of considered models, restoring R libraries to the state in which object was archived.Comment: Submitted to JSS in 2015, conditionally accepte

The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function

BACKGROUND: The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. Typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the PD-(D/E)XK superfamily were identified only after the corresponding structures were determined experimentally. Thus, it is tempting to speculate that among the uncharacterized protein families, there are potential nucleases that remain to be discovered, but their identification requires more sensitive tools than traditional PSI-BLAST searches. RESULTS: The low degree of amino acid conservation hampers the possibility of identification of new members of the PD-(D/E)XK superfamily based solely on sequence comparisons to known members. Therefore, we used a recently developed method HHsearch for sensitive detection of remote similarities between protein families represented as profile Hidden Markov Models enhanced by secondary structure. We carried out a comparison of known families of PD-(D/E)XK nucleases to the database comprising the COG and PFAM profiles corresponding to both functionally characterized as well as uncharacterized protein families to detect significant similarities. The initial candidates for new nucleases were subsequently verified by sequence-structure threading, comparative modeling, and identification of potential active site residues. CONCLUSION: In this article, we report identification of the PD-(D/E)XK nuclease domain in numerous proteins implicated in interactions with DNA but with unknown structure and mechanism of action (such as putative recombinase RmuC, DNA competence factor CoiA, a DNA-binding protein SfsA, a large human protein predicted to be a DNA repair enzyme, predicted archaeal transcription regulators, and the head completion protein of phage T4) and in proteins for which no function was assigned to date (such as YhcG, various phage proteins, novel candidates for restriction enzymes). Our results contributes to the reduction of "white spaces" on the sequence-structure-function map of the protein universe and will help to jump-start the experimental characterization of new nucleases, of which many may be of importance for the complete understanding of mechanisms that govern the evolution and stability of the genome

κ\kappa-Deformed Statistics and Classical Fourmomentum Addition Law

We consider $\kappa$-deformed relativistic symmetries described algebraically by modified Majid-Ruegg bicrossproduct basis and investigate the quantization of field oscillators for the $\kappa$-deformed free scalar fields on $\kappa$-Minkowski space. By modification of standard multiplication rule, we postulate the $\kappa$-deformed algebra of bosonic creation and annihilation operators. Our algebra permits to define the n-particle states with classical addition law for the fourmomenta in a way which is not in contradiction with the nonsymmetric quantum fourmomentum coproduct. We introduce $\kappa$-deformed Fock space generated by our $\kappa$-deformed oscillators which satisfy the standard algebraic relations with modified $\kappa$-multiplication rule. We show that such a $\kappa$-deformed bosonic Fock space is endowed with the conventional bosonic symmetry properties. Finally we discuss the role of $\kappa$-deformed algebra of oscillators in field-theoretic noncommutative framework.Comment: LaTeX, 12 pages. V2: second part of chapter 4 changed, new references and comments added. V3: formula (14) corrected. Some additional explanations added. V4: further comments about algebraic structure are adde

Canonical and Lie-algebraic twist deformations of κ\kappa-Poincare and contractions to κ\kappa-Galilei algebras

We propose canonical and Lie-algebraic twist deformations of $\kappa$-deformed Poincare Hopf algebra which leads to the generalized $\kappa$-Minkowski space-time relations. The corresponding deformed $\kappa$-Poincare quantum groups are also calculated. Finally, we perform the nonrelativistic contraction limit to the corresponding twisted Galilean algebras and dual Galilean quantum groups.Comment: 16 pages, no figures, v3: few changes provided - version for journal, v2: submitted incidentally, v4: the page numbers for all references in preprint version are provide

Molecular basis of tRNA recognition by the Elongator complex

The highly conserved Elongator complex modifies transfer RNAs (tRNAs) in their wobble base position, thereby regulating protein synthesis and ensuring proteome stability. The precise mechanisms of tRNA recognition and its modification reaction remain elusive. Here, we show cryo–electron microscopy structures of the catalytic subcomplex of Elongator and its tRNA-bound state at resolutions of 3.3 and 4.4 Å. The structures resolve details of the catalytic site, including the substrate tRNA, the iron-sulfur cluster, and a SAM molecule, which are all validated by mutational analyses in vitro and in vivo. tRNA binding induces conformational rearrangements, which precisely position the targeted anticodon base in the active site. Our results provide the molecular basis for substrate recognition of Elongator, essential to understand its cellular function and role in neurodegenerative diseases and cancer

Polish Society of Gynecology and Obstetrics statement on safety measures and performance of ultrasound examinations in obstetrics and gynecology during the SARS-CoV-2 pandemic

We present recommendations on performance and safety measures of ultrasound examinations in obstetrics and gynecologyduring the SARS COV-2 pandemic. The statement was prepared based on the current knowledge on the coronavirusby the Ultrasound Section of the Polish Society of Obstetrics and Gynecology. It has to be noted that the presented guidanceis based on limited evidence and is primarily based on experiences published by authors from areas most affected bythe virus thus far, such as China, Singapore, Hong Kong, and Italy. We realize that the pandemic situation is very dynamic.New data is published every day. Despite the imposed limitations related to the necessity of social distancing, it is crucialto remember that providing optimal care in safe conditions should remain the primary goal of healthcare providers. Weplan to update the current guidelines as the situation develops

Cryo-EM structure of the fully assembled elongator complex

Transfer RNA (tRNA) molecules are essential to decode messenger RNA codons during protein synthesis. All known tRNAs are heavily modified at multiple positions through post-transcriptional addition of chemical groups. Modifications in the tRNA anticodons are directly influencing ribosome decoding and dynamics during translation elongation and are crucial for maintaining proteome integrity. In eukaryotes, wobble uridines are modified by Elongator, a large and highly conserved macromolecular complex. Elongator consists of two subcomplexes, namely Elp123 containing the enzymatically active Elp3 subunit and the associated Elp456 hetero-hexamer. The structure of the fully assembled complex and the function of the Elp456 subcomplex have remained elusive. Here, we show the cryo-electron microscopy structure of yeast Elongator at an overall resolution of 4.3 Å. We validate the obtained structure by complementary mutational analyses in vitro and in vivo. In addition, we determined various structures of the murine Elongator complex, including the fully assembled mouse Elongator complex at 5.9 Å resolution. Our results confirm the structural conservation of Elongator and its intermediates among eukaryotes. Furthermore, we complement our analyses with the biochemical characterization of the assembled human Elongator. Our results provide the molecular basis for the assembly of Elongator and its tRNA modification activity in eukaryotes

Preparation and property-performance relationships in samarium-doped ceria nanopowders for solid oxide fuel cell electrolytes

In a systematic study, Samarium doped ceria (SDC) nanopowders, SmxCe1-xO2-x/2 (x = 0.1, 0.2 or 0.3), were prepared by a low temperature citrate complexation route. The synthesis and crystallisation of the SDC powders were followed by thermochemical techniques (TGA/DTA). X-ray diffraction, elemental analysis, specific surface area determination (BET) and electron microscopy (SEM and TEM). Mean crystallite sizes were found to be around 10 nm for all compositions calcined at 500 degrees C. Dense electrolyte bodies were prepared at 1300 degrees C, 1400 degrees C and 1450 degrees C using two sintering times, 4 h or 6 h. Densities of 91-97% of theoretical were obtained, with a marked improvement in density on going from 1300 degrees C to higher sintering temperatures. Grain size analysis was conducted using SEM. Grain size distributions were related to %Sm and sintering conditions. Impedance spectroscopy was used to determine the total, bulk and grain boundary conductivities, the related activation energies and enthalpies of defect association and ion migration. Sintering at 1400 degrees C/6 h or 1450 degrees C/4 h gave superior grain structure and conductivity, with oversintering occurring after more severe treatments. At 600 degrees C the highest total ionic conductivity was 1.81 x 10(-2) S cm(-1) for Sm0.2Ce0.8O1.9. The relationships between chemical composition, sintering parameters, grain structure and electrochemical performance are discussed. (C) 2010 Elsevier B.V. All rights reserved.</p