bluuebunny/crossref_metadata_2025 huggingface dataset:
KMC 2: fast and resource-frugal k-mer counting
Authors: Deorowicz Sebastian , Kokot Marek , Grabowski Szymon , Debudaj-Grabysz Agnieszka
Published: January 2015

Motivation: Building the histogram of occurrences of every k-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of k-mer counting. Its applications include developing de Bruijn graph genome assemblers, fast multiple sequence alignment and repeat detection. The tremendous amounts of NGS data require fast algorithms for k-mer counting, preferably using moderate amounts of memory.

Results: We present a novel method for k-mer counting, on large datasets about twice faster than the strongest competitors (Jellyfish 2, KMC 1), using about 12 GB (or less) of RAM. Our disk-based method bears some resemblance to MSPKmerCounter, yet replacing the original minimizers with signatures (a carefully selected subset of all minimizers) and using (k, x)-mers allows to significantly reduce the I/O and a highly parallel overall architecture allows to achieve unprecedented processing speeds. For example, KMC 2 counts the 28-mers of a human reads collection with 44-fold coverage (106 GB of compressed size) in about 20 min, on a 6-core Intel i7 PC with an solid-state disk.

Availability and implementation: KMC 2 is freely available at http://sun.aei.polsl.pl/kmc.

Contact: sebastian.deorowicz@polsl.pl

Supplementary information: Supplementary data are available at Bioinformatics online.
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Authors: Li Dinghua , Liu Chi-Man , Luo Ruibang , Sadakane Kunihiko , Lam Tak-Wah
Published: January 2015

Summary: MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252 Gbps in 44.1 and 99.6 h on a single computing node with and without a graphics processing unit, respectively. MEGAHIT assembles the data as a whole, i.e. no pre-processing like partitioning and normalization was needed. When compared with previous methods on assembling the soil data, MEGAHIT generated a three-time larger assembly, with longer contig N50 and average contig length; furthermore, 55.8% of the reads were aligned to the assembly, giving a fourfold improvement.

Availability and implementation: The source code of MEGAHIT is freely available at https://github.com/voutcn/megahit under GPLv3 license.

Contact:  rb@l3-bioinfo.com or twlam@cs.hku.hk

Supplementary information: Supplementary data are available at Bioinformatics online.
Intronic regions of plant genes potentially encode RDR (RNA-dependent RNA polymerase)-dependent small RNAs
Authors: Qin Jingping , Ma Xiaoxia , Yi Zili , Meng Yijun , Tang Zhonghai
Published: January 2015

The opinion is put forward here that certain intronic regions of plant genes could be converted to double-stranded RNA precursors for sRNA production through an RDR-dependent pathway.
Role of the Egami Score in Predicting Intravenous Immunoglobulin Resistance in Kawasaki Disease Among Different Ethnicities
Authors: Loomba Rohit S. , Raskin Alexander , Gudausky Todd M. , Kirkpatrick Edward
Published: January 2015

Early treatment with intravenous immunoglobulin (IVIG) is necessary to help reduce the risk of coronary artery abnormalities, such as coronary artery aneurysms and to help alleviate symptoms, in Kawasaki disease. Some patients, however, do not respond to an initial dose of IVIG and require additional doses. Prediction of these IVIG nonresponders may be of assistance in altering initial therapy to make it more effective. The Egami score has been validated in the Japanese population to predict IVIG nonresponders but has shown to be ineffective in US populations. This study evaluates the Egami score in a Midwest US population, subdividing patients by race and the diagnosis of typical or atypical type of Kawasaki disease. Patients were included in the study if they met criteria for Kawasaki disease and received IVIG in the inpatient setting. A total of 182 patients were studied, and in all studied groups, the Egami score had poor sensitivity at predicting IVIG nonresponders. Sensitivity of the score differed between races and differed between typical and atypical Kawasaki disease. The Egami score, as well as other systems, have been validated to predict IVIG nonresponders. These, however, lack sensitivity in the US population. Other scores developed in the United States have also lacked sensitivity, likely due to the absence of race or Kawasaki disease classification as variables. The development of a sensitive scoring system to predict IVIG nonresponders in US populations will require the incorporation of race and Kawasaki disease classification, factors that seem to alter IVIG response.
Use of a Feeding Bundle Appears to Reduce Central Line Utilization in Neonates
Authors: Tauber Kate A. , Graziano Pauline , Graffunder Eileen , Horgan Michael
Published: January 2015

We investigated whether a standardized feeding bundle reduces central line utilization in very low birth weight neonates. A chart review of infants ≤1500 g requiring a central line was prepared for 2009 to 2012. Infants were stratified into 3 weight groups: ≤750 g, 751 to 1000 g, and 1001 to 1500 g. The number of central line–associated bloodstream infections (CLABSIs) was recorded. Central line utilization decreased in all of the groups: 0.45 to 0.28 in ≤750 g infants, 0.4 to 0.27 in 751 to 1000 g infants, and 0.39 to 0.3 in 1001 to 1500 g infants (all of the P < 0.001). The CLABSIs rate was unchanged. Implementation of a feeding bundle decreased central line utilization. A feeding bundle had no effect on the rate of CLABSIs.
Impact of Intestinal Rehabilitation Program and Its Innovative Therapies on the Outcome of Intestinal Transplant Candidates
Authors: Avitzur Yaron , Wang Jenny Y. , de Silva Nicole T. , Burghardt Karolina M. , DeAngelis Maria , Grant David , Ng Vicky L. , Jones Nicola , Wales Paul W.
Published: January 2015

Objectives:

The outcome of children with intestinal failure has improved during the past decade following the introduction of novel therapies by dedicated intestinal rehabilitation programs (IRP). The aim of the present study was to assess the impact of IRP on the outcome of intestinal transplant (IT) candidates and the transplant waiting list.

Methods:

A retrospective cohort study of children assessed for IT (n = 84) during a 10‐year period. Comparisons were made among the following 3 time periods: before the establishment of our center's IRP (1999–2002; n = 33), early IRP (2003–2005; n = 18), and late IRP (2006–2009; n = 33). The following endpoints were used: patient outcome following IT assessment (not listed, listed and removed from the list, received transplant, died while on the list), patient characteristics at IT assessment, and patient status at the end of the study.

Results:

The late‐IRP era was associated with an increase in patients who were not listed (42% vs 28% at other periods, P = NS) and patients who were removed from the IT waiting list because of clinical improvement (P < 0.0005), and a decrease in those who died before transplant (15% vs >60% at other periods, P < 0.0005). The cause of death shifted from traditional causes such as liver failure or sepsis to other comorbid conditions (P < 0.005). Improved liver function at listing was also observed during late IRP (P < 0.005).

Conclusions:

Treatment by IRP, coupled with recent advances in the medical management of intestinal failure, is associated with improved survival and outcome of patients waiting for IT, and may lead to overall reduction in the number of IT in the future.
Nearest-neighbour clusters as a novel technique for assessing group associations
Authors: Rands Sean A.
Published: January 2015

When all the individuals in a social group can be easily identified, one of the simplest measures of social interaction that can be recorded is nearest-neighbour identity. Many field studies use sequential scan samples of groups to build up association metrics using these nearest-neighbour identities. Here, I describe a simple technique for identifying clusters of associated individuals within groups that uses nearest-neighbour identity data. Using computer-generated datasets with known associations, I demonstrate that this clustering technique can be used to build data suitable for association metrics, and that it can generate comparable metrics to raw nearest-neighbour data, but with much less initial data. This technique could therefore be of use where it is difficult to generate large datasets. Other situations where the technique would be useful are discussed.
Singlet lenses free of all orders of spherical aberration
Authors: Valencia-Estrada Juan Camilo , Flores-Hernández Ricardo Benjamín , Malacara-Hernández Daniel
Published: January 2015

This paper describes a method to design families of singlet lenses free of all orders of spherical aberration. These lenses can be mass produced according to Schwarzschild's formula and therefore one can find many practical applications. The main feature of this work is the application of an analysis that can be extended to grazing or maximum incidence on the first surface. Also, here, the authors present some developments that corroborate geometrical optics results, along with the axial thick lensmaker's formula, which can be applicable to any pair of finite conjugate planes for any lens shape (bending) and can be used instead of the classical thick lensmaker's formula, which always assumes that the object is at infinity, to attain better accuracy.
How to calculate all point symmetries of linear and linearizable differential equations
Authors: Gray Robert J.
Published: January 2015

The systematic method for calculating all point symmetries of partial differential equations (PDEs) with non-trivial Lie point symmetry algebras does not currently apply to linear PDEs. Consider any given locally solvable system of linear homogeneous PDEs, each of order 2 or higher, of general Kovalevskaya form. Suppose that its Lie point symmetry generators' characteristics are linear in the dependent variables, while those that are homogeneous of degree 1 in the dependent variables contain a finite number of arbitrary parameters (this is common for systems that arise from applications). Herein, every point symmetry is shown to be projectable/fibre-preserving: the transformed independent variables depend only on the original independent variables. Moreover, two (conditional) Lie-algebraic characterizations of the generators of scalings and superpositions of solutions are derived. One of them holds if the system cannot be decoupled (with a smooth, locally invertible, linear change of dependent variables). If any such characterization holds, every point symmetry maps the dependent variables to functions that are linear in the original dependent variables. The aforementioned systematic method is adapted to calculate these symmetries. This version of the method also applies to linearizable systems.
Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring
Authors: Dion-Côté Anne-Marie , Symonová Radka , Ráb Petr , Bernatchez Louis
Published: January 2015

Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish (
Coregonus clupeaformis
). We examined chromosomes in pure embryos, and healthy and malformed backcross embryos. While pure individuals displayed chromosome numbers corresponding to the expected diploid number (2
n
= 80), healthy backcrosses showed evidence of mitotic instability through an increased variance of chromosome numbers within an individual. In malformed backcrosses, extensive aneuploidy corresponding to multiples of the haploid number (1
n
= 40, 2
n
= 80, 3
n
= 120) was found, suggesting meiotic breakdown in their F
1
parent. However, no detectable chromosome rearrangements between parental forms were identified. Genomic instability through aneuploidy thus appears to contribute to reproductive isolation between dwarf and normal lake whitefish, despite their very recent divergence (approx. 15–20 000 generations). Our data suggest that genetic incompatibilities may accumulate early during speciation and limit hybridization between nascent species.
Frigidibacter albus gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from lake water
Authors: Li Ai-Hua , Zhou Yu-Guang
Published: January 2015

Three Gram-staining-negative, strictly aerobic, non-pigmented, non-motile, rod-shaped bacterial strains, SP32T ( = SLM-1T), SR68 ( = SLM-3) and SP95 ( = SLM-2), were isolated from two water samples of a cold-water lake in Xinjiang province, China. Growth was observed at 4–25 °C and pH 6.0–9.0, and optimum growth occurred at 18–20 °C and at pH 7.0–7.5. Phylogenetic analysis of 16S rRNA gene sequences revealed that these isolates belonged to the family

Rhodobacteraceae

, but formed an evolutionary lineage distinct from other species of this family with validly published names. Strain SP32T showed the highest 16S rRNA gene sequence similarity (96.7 %) to

Rhodobacter veldkampii

ATCC 35703T, and the similarity to members of the genera

Defluviimonas

,

Haematobacter

and

Pseudorhodobacter

was respectively 95.8–96.4, 96.0–96.1 and 95.3–96.1 %. The genomic DNA G+C content of strain SP32T was 67.6 mol%. The major fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and11-methyl C18 : 1ω7c. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, one unidentified glycolipid and one unidentified polar lipid were the main polar lipids. Ubiquinone 10 (Q-10) was the sole respiratory quinone. Strain SP32T did not produce photosynthetic pigments and did not contain the gene pufM, by which it differed from the phototrophic species of the family

Rhodobacteraceae

. Based on its distinct phenotypic, chemotaxonomic and phylogenetic properties, strain SP32T represents a novel species in a novel genus within the family

Rhodobacteraceae

, for which we propose the name Frigidibacter albus gen. nov., sp. nov. The type strain of Frigidibacter albus is strain SP32T ( = SLM-1T = CGMCC 1.13995T = NBRC 109671T).
Revision of the taxonomic status of the species Rhizobium lupini and reclassification as Bradyrhizobium lupini comb. nov.
Authors: Peix Alvaro , Ramírez-Bahena Martha Helena , Flores-Félix José David , Alonso de la Vega Pablo , Rivas Raúl , Mateos Pedro F. , Igual José M. , Martínez-Molina Eustoquio , Trujillo Martha E. , Velázquez Encarna
Published: January 2015

The species

Rhizobium lupini

was isolated from Lupinus nodules and included in the Approved Lists of Bacterial Names in 1980. Nevertheless, on the basis of the analysis of the type strain of this species available in DSMZ, DSM 30140T, whose 16S rRNA gene was identical to that of the type strain of

Bradyrhizobium japonicum

,

R. lupini

was considered a later synonym of this species. In this study we confirmed that the strain DSM 30140T belongs to the species

B. japonicum

, but also that it cannot be the original strain of

R. lupini

because this species effectively nodulated Lupinus whereas strain DSM 30140T was able to nodulate soybean but not Lupinus. Since the original type strain of

R. lupini

was deposited into the USDA collection by L. W. Erdman under the accession number USDA 3051T we analysed the taxonomic status of this strain showing that although it belongs to the genus

Bradyrhizobium

instead of genus

Rhizobium

, it is phylogenetically distant from

B. japonicum

and closely related to

Bradyrhizobium canariense

. The type strains

R. lupini

USDA 3051T and

B. canariense

BTA-1T share 16S rRNA, recA and glnII gene sequences with similarities of 99.8 %, 96.5 % and 97.1 %, respectively. They presented a DNA–DNA hybridization value of 36 % and also differed in phenotypic characteristics and slightly in the proportions of some fatty acids. Therefore we propose the reclassification of the species

Rhizobium lupini

as Bradyrhizobium lupini comb. nov. The type strain is USDA 3051T ( = CECT 8630T = LMG 28514T).
NCBI BLAST + integrated into Galaxy
Authors: Cock Peter J. A. , Chilton John M. , Grüning Björn , Johnson James E. , Soranzo Nicola
Published: January 2015

Background

The NCBI BLAST suite has become ubiquitous in modern molecular biology, used for small tasks like checking capillary sequencing results of single PCR products through to genome annotation or even larger scale pan-genome analyses. For early adopters of the Galaxy web-based biomedical data analysis platform, integrating BLAST was a natural step for sequence comparison workflows.

Findings

The command line NCBI BLAST+ tool suite was wrapped for use within Galaxy, defining appropriate datatypes as needed, with the goal of making common BLAST tasks easy, and advanced tasks possible.

Conclusions

This effort has been come an informal international collaborative effort, and is deployed and used on Galaxy servers worldwide. Several example use-cases are described herein.
Break-seq reveals hydroxyurea-induced chromosome fragility as a result of unscheduled conflict between DNA replication and transcription
Authors: Hoffman Elizabeth A. , McCulley Andrew , Haarer Brian , Arnak Remigiusz , Feng Wenyi
Published: January 2015

We have previously demonstrated that in Saccharomyces cerevisiae replication, checkpoint inactivation via a mec1 mutation leads to chromosome breakage at replication forks initiated from virtually all origins after transient exposure to hydroxyurea (HU), an inhibitor of ribonucleotide reductase. Here we sought to determine whether all replication forks containing single-stranded DNA gaps have equal probability of producing double-strand breaks (DSBs) when cells attempt to recover from HU exposure. We devised a new methodology, Break-seq, that combines our previously described DSB labeling with next generation sequencing to map chromosome breaks with improved sensitivity and resolution. We show that DSBs preferentially occur at genes transcriptionally induced by HU. Notably, different subsets of the HU-induced genes produced DSBs in MEC1 and mec1 cells as replication forks traversed a greater distance in MEC1 cells than in mec1 cells during recovery from HU. Specifically, while MEC1 cells exhibited chromosome breakage at stress-response transcription factors, mec1 cells predominantly suffered chromosome breakage at transporter genes, many of which are the substrates of those transcription factors. We propose that HU-induced chromosome fragility arises at higher frequency near HU-induced genes as a result of destabilized replication forks encountering transcription factor binding and/or the act of transcription. We further propose that replication inhibitors can induce unscheduled encounters between replication and transcription and give rise to distinct patterns of chromosome fragile sites.
The design and structural characterization of a synthetic pentatricopeptide repeat protein
Authors: Gully Benjamin S. , Shah Kunal R. , Lee Mihwa , Shearston Kate , Smith Nicole M. , Sadowska Agata , Blythe Amanda J. , Bernath-Levin Kalia , Stanley Will A. , Small Ian D. , Bond Charles S.
Published: January 2015

Proteins of the pentatricopeptide repeat (PPR) superfamily are characterized by tandem arrays of a degenerate 35-amino-acid α-hairpin motif. PPR proteins are typically single-stranded RNA-binding proteins with essential roles in organelle biogenesis, RNA editing and mRNA maturation. A modular, predictable code for sequence-specific binding of RNA by PPR proteins has recently been revealed, which opens the door to thede novodesign of bespoke proteins with specific RNA targets, with widespread biotechnological potential. Here, the design and production of a synthetic PPR protein based on a consensus sequence and the determination of its crystal structure to 2.2 Å resolution are described. The crystal structure displays helical disorder, resulting in electron density representing an infinite superhelical PPR protein. A structural comparison with related tetratricopeptide repeat (TPR) proteins, and with native PPR proteins, reveals key roles for conserved residues in directing the structure and function of PPR proteins. The designed proteins have high solubility and thermal stability, and can form long tracts of PPR repeats. Thus, consensus-sequence synthetic PPR proteins could provide a suitable backbone for the design of bespoke RNA-binding proteins with the potential for high specificity.
Biochemical and structural investigation of two paralogous glycoside hydrolases fromZobellia galactanivorans: novel insights into the evolution, dimerization plasticity and catalytic mechanism of the GH117 family
Authors: Ficko-Blean Elizabeth , Duffieux Delphine , Rebuffet Étienne , Larocque Robert , Groisillier Agnes , Michel Gurvan , Czjzek Mirjam
Published: January 2015

The family 117 glycoside hydrolase (GH117) enzymes have exo-α-1,3-(3,6-anhydro)-L-galactosidase activity, removing terminal nonreducing α-1,3-linked 3,6-anhydro-L-galactose residues from their red algal neoagarose substrate. These enzymes have previously been phylogenetically divided into clades, and only the clade A enzymes have been experimentally studied to date. The investigation of two GH117 enzymes, Zg3615 and Zg3597, produced by the marine bacteriumZobellia galactanivoransreveals structural, biochemical and further phylogenetic diversity between clades. A product complex with the unusual β-3,6-anhydro-L-galactose residue sheds light on the inverting catalytic mechanism of the GH117 enzymes as well as the structure of this unique sugar produced by hydrolysis of the agarophyte red algal cell wall.
Exploring the speed and performance of molecular replacement withAMPLEusingQUARK ab initioprotein models
Authors: Keegan Ronan M. , Bibby Jaclyn , Thomas Jens , Xu Dong , Zhang Yang , Mayans Olga , Winn Martyn D. , Rigden Daniel J.
Published: January 2015

AMPLEclusters and truncatesab initioprotein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the differentab initiomodelling programsQUARKandROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced byPhaserafter only 5 min perform surprisingly well, improving the prospects forin situstructure solution byAMPLEduring synchrotron visits. Taken together, the results show the potential forAMPLEto run more quickly and successfully solve more targets than previously suspected.
Biochemical and structural study ofArabidopsishexokinase 1
Authors: Feng Juan , Zhao Shun , Chen Xuemin , Wang Wenda , Dong Wei , Chen Jinghua , Shen Jian-Ren , Liu Lin , Kuang Tingyun
Published: January 2015

Hexokinase 1 fromArabidopsis thaliana(AtHXK1) plays a dual role in glycolysis and sugar sensing for vital metabolic and physiological processes. The uncoupling of glucose signalling from glucose metabolism was demonstrated by the analysis of two mutants (AtHXK1G104DandAtHXK1S177A) that are catalytically inactive but still functional in signalling. In this study, substrate-binding experiments indicate that the two catalytically inactive mutants have a high affinity for glucose, and an ordered substrate-binding mechanism has been observed for wild-typeAtHXK1. The structure ofAtHXK1 was determined both in its inactive unliganded form and in its active glucose-bound form at resolutions of 1.8 and 2.0 Å, respectively. These structures reveal a domain rearrangement ofAtHXK1 upon glucose binding. The 2.1 Å resolution structure ofAtHXK1S177Ain the glucose-bound form shows similar glucose-binding interactions as the wild type. A glucose-sensing network has been proposed based on these structures. Taken together, the results provide a structural explanation for the dual functions ofAtHXK1.
Indexing amyloid peptide diffraction from serial femtosecond crystallography: new algorithms for sparse patterns
Authors: Brewster Aaron S. , Sawaya Michael R. , Rodriguez Jose , Hattne Johan , Echols Nathaniel , McFarlane Heather T. , Cascio Duilio , Adams Paul D. , Eisenberg David S. , Sauter Nicholas K.
Published: January 2015

Still diffraction patterns from peptide nanocrystals with small unit cells are challenging to index using conventional methods owing to the limited number of spots and the lack of crystal orientation information for individual images. New indexing algorithms have been developed as part of theComputational Crystallography Toolbox(cctbx) to overcome these challenges. Accurate unit-cell information derived from an aggregate data set from thousands of diffraction patterns can be used to determine a crystal orientation matrix for individual images with as few as five reflections. These algorithms are potentially applicable not only to amyloid peptides but also to any set of diffraction patterns with sparse properties, such as low-resolution virus structures or high-throughput screening of still images captured by raster-scanning at synchrotron sources. As a proof of concept for this technique, successful integration of X-ray free-electron laser (XFEL) data to 2.5 Å resolution for the amyloid segment GNNQQNY from the Sup35 yeast prion is presented.
Protein–RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions
Authors: Tishchenko Svetlana , Kostareva Olga , Gabdulkhakov Azat , Mikhaylina Alisa , Nikonova Ekaterina , Nevskaya Natalia , Sarskikh Alena , Piendl Wolfgang , Garber Maria , Nikonov Stanislav
Published: January 2015

Ribosomal protein L1, as part of the L1 stalk of the 50S ribosomal subunit, is implicated in directing tRNA movement through the ribosome during translocation. High-resolution crystal structures of four mutants (T217V, T217A, M218L and G219V) of the ribosomal protein L1 fromThermus thermophilus(TthL1) in complex with a specific 80 nt fragment of 23S rRNA and the structures of two of these mutants (T217V and G219V) in the RNA-unbound form are reported in this work. All mutations are located in the highly conserved triad Thr-Met-Gly, which is responsible for about 17% of all protein–RNA hydrogen bonds and 50% of solvent-inaccessible intermolecular hydrogen bonds. In the mutated proteins without bound RNA the RNA-binding regions show substantial conformational changes. On the other hand, in the complexes with RNA the structures of the RNA-binding surfaces in all studied mutants are very similar to the structure of the wild-type protein in complex with RNA. This shows that formation of the RNA complexes restores the distorted surfaces of the mutant proteins to a conformation characteristic of the wild-type protein complex. Domain I of the mutated TthL1 and helix 77 of 23S rRNA form a rigid body identical to that found in the complex of wild-type TthL1 with RNA, suggesting that the observed relative orientation is conserved and is probably important for ribosome function. Analysis of the complex structures and the kinetic data show that the number of intermolecular contacts and hydrogen bonds in the RNA–protein contact area does not correlate with the affinity of the protein for RNA and cannot be used as a measure of affinity.
Room-temperature serial crystallography at synchrotron X-ray sources using slowly flowing free-standing high-viscosity microstreams
Authors: Botha Sabine , Nass Karol , Barends Thomas R. M. , Kabsch Wolfgang , Latz Beatrice , Dworkowski Florian , Foucar Lutz , Panepucci Ezequiel , Wang Meitian , Shoeman Robert L. , Schlichting Ilme , Doak R. Bruce
Published: January 2015

Recent advances in synchrotron sources, beamline optics and detectors are driving a renaissance in room-temperature data collection. The underlying impetus is the recognition that conformational differences are observed in functionally important regions of structures determined using crystals kept at ambient as opposed to cryogenic temperature during data collection. In addition, room-temperature measurements enable time-resolved studies and eliminate the need to find suitable cryoprotectants. Since radiation damage limits the high-resolution data that can be obtained from a single crystal, especially at room temperature, data are typically collected in a serial fashion using a number of crystals to spread the total dose over the entire ensemble. Several approaches have been developed over the years to efficiently exchange crystals for room-temperature data collection. These includein situcollection in trays, chips and capillary mounts. Here, the use of a slowly flowing microscopic stream for crystal delivery is demonstrated, resulting in extremely high-throughput delivery of crystals into the X-ray beam. This free-stream technology, which was originally developed for serial femtosecond crystallography at X-ray free-electron lasers, is here adapted to serial crystallography at synchrotrons. By embedding the crystals in a high-viscosity carrier stream, high-resolution room-temperature studies can be conducted at atmospheric pressure using the unattenuated X-ray beam, thus permitting the analysis of small or weakly scattering crystals. The high-viscosity extrusion injector is described, as is its use to collect high-resolution serial data from native and heavy-atom-derivatized lysozyme crystals at the Swiss Light Source using less than half a milligram of protein crystals. The room-temperature serial data allowde novostructure determination. The crystal size used in this proof-of-principle experiment was dictated by the available flux density. However, upcoming developments in beamline optics, detectors and synchrotron sources will enable the use of true microcrystals. This high-throughput, high-dose-rate methodology provides a new route to investigating the structure and dynamics of macromolecules at ambient temperature.
Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression
Authors: Shevtsov M. B. , Streeter S. D. , Thresh S.-J. , Swiderska A. , McGeehan J. E. , Kneale G. G.
Published: January 2015

In a wide variety of bacterial restriction–modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal.
The relationship between Renminbi’s exchange rate and East Asia currencies before and after the “financial crisis”
Authors: Xu Xiangyun , Wu Songyang , Wu Ye
Published: January 2015

Purpose

– The purpose of this paper is to analyze the “following” behavior of six currencies in East Asia to RMB before and after the “financial crisis”.

Design/methodology/approach

– Using foreign exchange spot rate data from 2005 to 2013, the authors investigate the dynamic relationship of RMB and six East Asia currencies with method of DCC-GARCH and quantile regression.

Findings

– The authors get such conclusions: first, most currencies indeed “follow” RMB in whole sample period but the correlation is “time-varying”; second, the degree of co-movement increased as a whole, which reflects that the influence of China in East Asia rose continuously; third, the East Asian currencies behaved differently before the crisis, but reveal some similarities after the crisis, and prefer to “follow” when RMB depreciates and reluctant to follow when RMB appreciates at a comparatively large degree. The authors argue that it may be related to the different macroeconomic environment faced by East Asia region before and after the crisis, the rising economic influence of China and the development of RMB internationalization’s practice.

Originality/value

– The effort could strength the understanding to the “following” behavior of East Asia currencies to RMB, the authors also point out that RMB has been as regional currency anchor, but the role of anchor is unstable, and is affected by international economic circumstance, China should adapt some methods to strength RMB’s influence to East Asia currency.
The roles of accounting data in equity valuation: evidence from China
Authors: Wang Tiandong , Zhang Tianxi
Published: January 2015

Purpose

– The purpose of this paper is to examine the roles of earnings and book value (BV) in equity valuation.

Design/methodology/approach

– The authors apply model’s explanatory power to analyze the roles of accounting data and test the hypotheses empirically with a sample of Chinese listed companies between 2004 and 2010.

Findings

– The authors find that impact of accounting data on equity value is also dependent on profitability, but the behavior is non-monotonic. In the intermediate-profitability range, explanatory power of both earnings capitalization model and balance sheet model reach the peak, there are no significant differences between them. In the low-profitability range (small or negative profitability), explanatory power of balance sheet model is larger than earnings capitalization model. In the high-profitability range, explanatory power of balance sheet model is less than earnings capitalization model.

Research limitations/implications

– The results support that the role of BV is more stable in equity valuation. Moreover, this outcome provides reference for improving existing valuation model and setting accounting standard, and provides some empirical evidence for the practical application of BV in equity valuation.

Originality/value

– Existing studies treat earnings as main variable of equity valuation, and BV is only added as a supplement. This paper compares roles of accounting earnings and BV in equity valuation, especially investigates the influence of BV in equity valuation, and fills up the deficiency in the related literature.
Evaluating a rugby sport intervention programme for young offenders
Authors: Williams Dave , Collingwood Leann , Coles James , Schmeer Stefanie
Published: January 2015

Purpose

– Interventions intended to aid offender re-entry, rehabilitation and desistence based around specific sports and championed by sporting institutions have been introduced in custodial settings. Though research evaluating these is positive (Meek, 2012), conclusions are often hampered by the absence of control groups in such work. The purpose of this paper is to evaluate the Saracens “Get Onside” rugby-based intervention at HMP YOI Feltham, while employing a non-randomised control group.

Design/methodology/approach

– In total, 24 young offenders took part. Those in the treatment condition experienced a ten-week course which included a range of activities leading to accredited awards, exercises in functional skills in literacy/numeracy and 72 hours of rugby sessions. Those in the control condition were matched on key static factors, crime attitudes and aggression. Self-reported measures of pro-crime attitudes, aggression, self-esteem, and impulsivity were taken once before the start, once during, and at the end of the course for both groups.

Findings

– As predicted, self-reported scores measuring attitudes towards aggression and crime did differ significantly across groups, with those experiencing the intervention showing more positive values by the end of treatment compared with others. However, measures of impulsiveness and self-esteem showed no change.

Research limitations/implications

– Revisions are suggested in respect of both the self-esteem and impulsivity measures, and future work needs better control over the match between treatment and comparison groups.

Originality/value

– Concerns over the potentially iatrogenic effects of contact sport interventions with offender groups may be misplaced, and the benefits of sporting interventions are replicated in a between groups design.
A predictive model of criminality in civil psychiatric populations
Authors: Evans Laura , Ioannou Maria , Hammond Laura
Published: January 2015

Purpose

– The purpose of this paper is to develop a predictive model of criminal risk in civil psychiatric populations, by determining the relative impacts of psychopathy, drug use, impulsivity and intelligence on levels of criminality.

Design/methodology/approach

– The sample consisted of 871 civil psychiatric patients, selected from the MacArthur Violence Risk Assessment Study, who had been diagnosed with a mental illness or personality disorder, and hospitalised less than 21 days. Each participant was administered the Hare Psychopathy Checklist Screening Version (PCL:SV), Barratt Impulsiveness Scale (BIS-11) and the Wechsler Adult Intelligence Scale (WAIS-R). In addition, information on background demographics, drug use and criminality was obtained via a self-report questionnaire.

Findings

– Pearson correlations identified significant positive relationships between past arrests, psychopathy, impulsivity and drug use. Intelligence was negatively related to past arrests. Multiple regressions identified a significant main effect for Factor 2 psychopathy on past arrests when controlling for all covariates, but not for Factor 1 psychopathy, intelligence or impulsivity. Drug use and gender had small univariate effects.

Research limitations/implications

– It is suggested that future research investigates the influence of specific mental disorders on different types of offending.

Originality/value

– By investigating predictors of criminal behaviour in civil psychiatric patients, the present study makes valuable contributions to the research literature, enhancing our theoretical understanding of the relationships between psychopathy and criminality/recidivism. It also has notable implications in applied practice, for example in the development and refinement of risk assessment methods.
Women bus drivers and organizational change
Authors: Sanchez de Miguel Manuel , Lizaso Izarne , Larranaga Maider , Arrospide Juan Jose
Published: January 2015

Purpose

– The purpose of this paper is to discuss the gender practices of a female urban bus driver who retired after 40 years (1967-2007) in an urban bus company in northern Spain. The main objective of this study was to explore and understand the move from irreflexive to reflexive practices from a gender perspective, and to uncover new key aspects relating to the influence of women in organizational changes.

Design/methodology/approach

– This qualitative exploratory study (interpretative phenomenological analysis (IPA)) contains semi-structured interviews which explore, using a process of analytic induction, the personal- and work-related experiences of a woman who was a pioneer in the traditionally male-dominated field of urban bus services. In order to obtain a broader overview of the organization, and using the same method, four other female bus drivers from the same company were also interviewed, along with the personnel manager.

Findings

– Three different situations are presented. The first summarizes the woman’s personal motivations and hesitations during the 1960s regarding her decision to become a bus driver, occurring during her adolescence and pre-professional phase; the second illustrates the organizational and social reactions triggered by the (visible) presence of a lone woman in a traditionally male professional environment (resistance); and finally, the third situation shows the empowerment and organizational change which occurred, focussing on the possible deconstruction of the masculine hegemony at the heart of the organization.

Originality/value

– The IPA points to a new level of visibility of this transgressed traditional role, which combined both individual and collective actions. Her experiences recount how she overcame individual, organizational and social barriers. The authors suggest a new interpretation of this visibility, enabling us to imagine gender practice as an intersection of people, organizational change and society.
Eco-innovation practices
Authors: Mele Cristina , Russo-Spena Tiziana
Published: January 2015

Purpose

– The purpose of this paper is to examine eco-innovation practices within project networks. Eco-innovation practices involve systematic series of actions that integrate resources to create value.

Design/methodology/approach

– Using case research, the authors conducted an intensive study of innovation practices within project networks, using multiple sources of evidence to provide information to scholars and practitioners (Halinen and Tornroos, 2005). Analyzing practices facilitated an empirical investigation of how contextual elements shaped the social construction of eco-innovation.

Findings

– An empirical analysis of eight project networks identifies three eco-innovation practices: cleaning up the landscape, connecting life and work, and boosting the efficiency of inbound and outbound processes. A methodological framework based on this practice approach is used to discuss the main elements of the practices in question, including actors, actions, resources, and value.

Practical implications

– The practice-based approach (PBA) may help companies to make information and communication technology (ICT) more sustainable. By developing forms of eco-innovation that support project networks, companies can focus on holistic corporate performance, efficiency, and business value. Eco-innovation thus becomes a collective achievement that allows practitioners to appraise and critique the performance of their environmental practices, and that thereby allows them to constantly refine those practices.

Social implications

– The development and use of Green ICT solutions enable actors’ sense-making and sense-giving within ongoing social practices wherein macro-level phenomena, such as sustainability and environmental issues, are created and recreated through the micro-level actions of project network actors.

Originality/value

– This research extends beyond the more traditional issues of ecologically sound company operations and sustainable ICT use to address sustainable ways of doing business.
Examining the relationship between organizational change and financial loss
Authors: Mellert Lars Derek , Scherbaum Charles , Oliveira Justina , Wilke Bernd
Published: January 2015

Purpose

– Research on the effectiveness of organizational change initiatives tends to focus primarily on the positive benefits of organizational change including improved financial performance. Rarely are negative outcomes examined, such as financial losses resulting from change initiatives. However, negative outcomes are possible, common, and understudied. The purpose of this paper is to examine the relationship between organizational change and financial loss.

Design/methodology/approach

– The research used a database of insurance losses from a global reinsurance company over a 30-year period. Each loss event was examined to determine the cause of the loss, the amount of loss, and type of organizational change if any that preceded the loss.

Findings

– The results indicate that losses attributed to the organization and its employees are preceded by an organizational change initiative more often than not. In particular, the occurrence of losses attributable to the organization and its employees were preceded more often by organizational changes involving mergers, acquisitions and changes to ownership, changes involving downsizing, changes involving restructuring, but not changes to reporting relationships.

Originality/value

– This research represents one of the few studies to examine financial loss from a wide variety of different types of organizational change and the only that has examined these questions using data from insurance losses. Findings support the growing theoretical movement focussing on the risks of organizational change.
Leadership role and employee acceptance of change
Authors: Johannsdottir Lara , Olafsson Snjolfur , Davidsdottir Brynhildur
Published: January 2015

Purpose

– The change management literature on strategy implementation identifies different dimensions of resistance to change. The contrary view – that of dimensions of acceptance of change when implementing strategy – has received less attention. The purpose of this paper is to explore the implementation of environmental sustainability strategies by Nordic insurers, the role of leadership in implementing these changes, and employee acceptance of change.

Design/methodology/approach

– For achieving this purpose, this paper reports on an explanatory case study of Nordic non-life insurers, where interviews with insurance executives and specialists were the primary source of data.

Findings

– The authors have developed simple strategy maps, focusing on insurers’ own operations, product offerings, loss prevention and claims settlements, investments and influence on stakeholders, to show how common elements of environmental strategies are implemented within the insurance industry. The importance of leadership in organizational change is evident in the data, as well as in employees’ positive attitudes towards implementation of environmental sustainability strategies.

Originality/value

– The scientific contribution of this paper is the empirical mapping of a hitherto unexplored area of the implementation of environmental sustainability strategies within the Nordic insurance industry, highlighting the leadership role in implementing environmental sustainability strategies and the elements shaping employee acceptance of change when implementing environmental sustainability strategies.