bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic properties and magnetocaloric effect of the HoAgGa compound
Authors: da Silva L. M. , dos Santos A. O. , Coelho A. A. , Cardoso L. P.
Published: October 2013

Magnetic properties and magnetocaloric effect (MCE) of the HoAgGa compound are investigated by magnetization and heat capacity measurements. A giant reversible MCE was observed around TC = 7.2 K. The maximum values of magnetic entropy change and adiabatic temperature are found to be 16 J kg−1 K−1 and 6 K, respectively, with a refrigerant capacity value of 262 J kg−1 for field change of 5 T. These magnetocaloric parameters also remain large for a wide range of temperature above TC. The large MCE as well as no hysteresis loss make HoAgGa an attractive candidate for low temperature magnetic refrigerant.
Two resistive switching regimes in thin film manganite memory devices on silicon
Authors: Rubi D. , Tesler F. , Alposta I. , Kalstein A. , Ghenzi N. , Gomez-Marlasca F. , Rozenberg M. , Levy P.
Published: October 2013

Bipolar resistive switching in low cost n-Si/La2/3Ca1/3MnO3/M (M = Ti + Cu) devices was investigated. For low SET compliance currents (CC), an interfacial-related resistive switching mechanism, associated to the migration of oxygen vacancies close to the manganite/metal interface, is operative. Simulations using the voltage enhanced oxygen vacancies drift model validate our experimental results. When further increasing the CC, we have observed the onset of a second, filamentary, resistive switching regime with a concomitant collapse of the ON/OFF ratio. We finally demonstrate that it is possible to delay the onset of the filamentary regime by controlling the film thickness.
Evidence of two superconducting phases in Ca1−xLaxFe2As2
Authors: Sun Y. , Zhou W. , Cui L. J. , Zhuang J. C. , Ding Y. , Yuan F. F. , Bai J. , Shi Z. X.
Published: October 2013

Single crystals of Ca1−xLaxFe2As2 with x ranging from 0 to 0.25, have been grown and characterized by structural, transport, and magnetic measurements. Coexistence of two superconducting phases is observed, in which the phase with the lower superconducting transition temperature (Tc) has Tc ∼ 20 K and the higher Tc phase has Tc higher than 40 K. These data also delineate an x-T phase diagram in which the single magnetic/structural phase transition in undoped CaFe2As2 appears to split into two distinct phase transitions, both of which are suppressed with increasing La substitution. Superconductivity emerges when x is about 0.06 and coexists with the structural/magnetic transition until x is ∼ 0.13. With increasing concentration of La, the structural/magnetic transition is totally suppressed, and Tc reaches its maximum value of about 45 K for 0.15 ⩽ x ⩽ 0.19. A domelike superconducting region is not observed in the phase diagram, however, because no obvious over-doping region can be found. Two superconducting phases coexist in the x-T phase diagram of Ca1−xLaxFe2As2. The formation of the two separate phases and the origin of the high Tc in Ca1−xLaxFe2As2 have been studied and discussed in detail.
Employment, Entrepreneurship, and Citizenship in a Globalised Economy: The Chinese in Prato
Authors: Barbu Mirela , Dunford Michael , Weidong Liu
Published: October 2013

Since 2000 Prato's domestic textile sector has contracted in the face of international competition. From the 1990s a large Chinese community has emerged, and since 2000 the number of Chinese clothing enterprises has increased rapidly. In recent years tensions between the Italian and Chinese communities have increased, and police investigations have risen, in part due to perceptions of unfair Chinese competition and illegality. This paper examines these tensions, their roots in differing economic practices, regulatory frameworks, and cultural values, and considers the strategies of public authorities as they seek to improve economic performance, social integration, and political stability.
The Effect of Urban Form and Residential Cooling Energy Use in Sacramento, California
Authors: Ko Yekang , Radke John D
Published: October 2013

The impact of urban form on residential space-conditioning energy use has been controversial in recent planning literature. This study empirically evaluates the association between urban form and residential energy use, focusing particularly on residential electricity use for space cooling in the City of Sacramento, California. We characterize urban form, property conditions, and demographic and socioeconomic characteristics by applying spatial metrics embedded within a geographic information system where LiDAR data effectively include each building and the surrounding vegetation. A statistical model is applied to assess the relationship between these explanatory variables and the estimated summer air-conditioning energy use. Controlling for other variables, higher population density, east—west street orientation, higher green space density, larger vegetation on the east, south, and especially the west sides of houses, appears to have statistically significant effects on reducing summer cooling energy use. This study quantifies the built environment impact on the energy demand of air conditioning and informs planners as they craft urban planning and design policies for energy conservation.
The effects of salinity, turbidity and flow on fish biomass estimated acoustically in two tidal rivers
Authors: Matveev V. F. , Steven A. D. L.
Published: October 2013

Establishing drivers of fish abundance in estuaries is an important task of both theoretical and practical significance. Commercial catch data help explain large-scale variation in fish productivity; however, there is insufficient understanding of small-scale changes. We analysed correlations between acoustically estimated fish biomass (FB) and environmental variables, which included indices of primary productivity and physio-chemistry in a coastal river system during four seasons. Spatial series of FB were obtained for the Logan River (main estuary) and the Albert River (tributary) located in South East Queensland, Australia. Most of the year, FB was significantly higher in the Albert River. Annual means for discharge, salinity and pH were significantly lower, whereas phosphorus concentrations were higher in the Albert River. Out of 15 hydrological variables tested, FB was strongly correlated only with salinity, conductivity and turbidity. In the Albert River, where fish were larger, as indicated by greater target strengths, FB was positively correlated with river discharge. Our results suggest that salinity and turbidity can be important seasonal drivers of fish abundance in communities dominated by Mugil spp. and Nematalosa erebi and that the flow-biomass relationship may appear independent of the effects of primary production.
Are graph databases ready for bioinformatics?
Authors: Have Christian Theil , Jensen Lars Juhl
Published: October 2013

Contact:  Lars.Juhl.Jensen@gmail.com
Frequent glycan structure mining of influenza virus data revealed a sulfated glycan motif that increased viral infection
Authors: Ichimiya Tomomi , Nishihara Shoko , Takase-Yoden Sayaka , Kida Hiroshi , Aoki-Kinoshita Kiyoko
Published: October 2013

Motivation: It is well known influenza viruses recognize and bind terminal sialic acid (SA) on glycans that are found on the cell surface. In this work, we used a data mining technique to analyze the glycan array data of influenza viruses to find novel glycan structures other than SA that may be involved in viral infection.

Results: In addition to SA structures noted previously, we noted the sulfated structures in the mining results. For verification, we overexpressed the sulfotransferase that is involved in synthesizing these structures, and we performed a viral infection experiment to assess changes in infection in these cells. In our results, we found that there is a 70-fold increase in these cells compared with the control. Thus, we have found a novel pattern in glycan structures that may be involved in viral infection.

Availability and implementation: The Glycan Miner Tool is available from the RINGS resource at http://www.rings.t.soka.ac.jp.

Contact: kkiyoko@soka.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish
Authors: Stegmaier Johannes , Shahid Maryam , Takamiya Masanari , Yang Lixin , Rastegar Sepand , Reischl Markus , Strähle Uwe , Mikut Ralf
Published: October 2013

Motivation: To reliably assess the effects of unknown chemicals on the development of fluorescently labeled sensory-, moto- and interneuron populations in the spinal cord of zebrafish, automated data analysis is essential.

Results: For the evaluation of a high-throughput screen of a large chemical library, we developed a new method for the automated extraction of quantitative information from green fluorescent protein (eGFP) and red fluorescent protein (RFP) labeled spinal cord neurons in double-transgenic zebrafish embryos. The methodology comprises region of interest detection, intensity profiling with reference comparison and neuron distribution histograms. All methods were validated on a manually evaluated pilot study using a Notch inhibitor dose-response experiment. The automated evaluation showed superior performance to manual investigation regarding time consumption, information detail and reproducibility.

Availability and implementation: Being part of GNU General Public Licence (GNU-GPL) licensed open-source MATLAB toolbox Gait-CAD, an implementation of the presented methods is publicly available for download at http://sourceforge.net/projects/zebrafishimage/.

Contact:  johannes.stegmaier@kit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Migration, residency, and homing of bluefin tuna in the western Mediterranean Sea
Authors: Fromentin Jean-Marc , Lopuszanski Daniel
Published: October 2013

This study presents the results of an electronic tagging programme on mature Atlantic bluefin tuna (ABFT) that has been conducted since 2007 offshore of the French Mediterranean Coast. The spatial distributions of ABFT showed little year-to-year variation and the fish concentrated in a small area of the central northwestern Mediterranean, where they may stay for several months. The individual tracks display sinuous trajectories in this area, indicating the possibility of feeding behaviour. No fish went out to the North Atlantic, but several fish displayed some migration to the southern western Mediterranean Sea during winter and the central Mediterranean during the spawning season. The homing behaviour of one fish after a full year as well as the back and forth of several fish further indicates that this restricted feeding area is probably persistent from year to year. We hypothesize that this area could result from local enrichment due to permanent mesoscale oceanographic features related to the North Mediterranean Current and the North Balearic front. The option of a spatial management, through marine protected areas, for a highly migratory species, such as ABFT, thus deserves more careful consideration because those species displayed complex spatial dynamics (e.g. homing), and population structure (e.g. several subpopulations of different sizes).
Metals and ionizing photons from dwarf galaxies
Authors: Salvadori S. , Tolstoy E. , Ferrara A. , Zaroubi S.
Published: October 2013

We estimate the potential contribution of M < 109 M⊙ dwarf galaxies to the reionization and early metal enrichment of the Milky Way environment, or circum-Galactic medium. Our approach is to use the observed properties of ancient stars (≳12 Gyr old) measured in nearby dwarf galaxies to characterize the star formation at high z. We use a merger-tree model for the build-up of the Milky Way, which self-consistently accounts for feedback processes, and which is calibrated to match the present-day properties of the Galaxy and its dwarf satellites. We show that the high-z analogues of nearby dwarf galaxies can produce the bulk of ionizing radiation (>80 per cent) required to reionize the Milky Way environment. Our fiducial model shows that the gaseous environment can be 50 per cent reionized at z ≈ 8 by galaxies with 107 M⊙ ≤ M < 108 M⊙. At later times, radiative feedback stops the star formation in these small systems, and reionization is completed by more massive dwarf galaxies by zrei = 6.4 ± 0.5. The metals ejected by supernova-driven outflows from M < 109 M⊙ dwarf galaxies almost uniformly fill the Milky Way environment by z ≈ 5, enriching it to Z ≈ 2 × 10−2 Z⊙. At z ≈ 2, these early metals are still found to represent the ≈50 per cent of the total mass of heavy elements in the circum-Galactic medium.
Ultrasonography of the Cervical Spine
Authors: van Eerd Maarten , Patijn Jacob , Sieben Judith M. , Sommer Mischa , Van Zundert Jan , van Kleef Maarten , Lataster Arno
Published: October 2013

Background:

Anatomical validation studies of cervical ultrasound images are sparse. Validation is crucial to ensure accurate interpretation of cervical ultrasound images and to develop standardized reliable ultrasound procedures to identify cervical anatomical structures. The aim of this study was to acquire validated ultrasound images of cervical bony structures and to develop a reliable method to detect and count the cervical segmental levels.

Methods:

An anatomical model of a cervical spine, embedded in gelatin, was inserted in a specially developed measurement device. This provided ultrasound images of cervical bony structures. Anatomical validation was achieved by laser light beams projecting the center of the ultrasound image on the cervical bony structures through a transparent gelatin.

Results:

Anatomically validated ultrasound images of different cervical bony structures were taken from dorsal, ventral, and lateral perspectives. Potentially relevant anatomical landmarks were defined and validated. Test/retest analysis for positioning showed a reproducibility with an intraclass correlation coefficient for single measures of 0.99. Besides providing validated ultrasound images of bony structures, this model helped to develop a method to detect and count the cervical segmental levels in vivo at long-axis position, in a dorsolateral (paramedian) view at the level of the laminae, starting from the base of the skull and sliding the ultrasound probe caudally.

Conclusions:

Ultrasound bony images of the cervical vertebrae were validated with an in vitro model. Anatomical bony landmarks are the mastoid process, the transverse process of C1, the tubercles of C6 and C7, and the cervical laminae. Especially, the cervical dorsal laminae serve best as anatomical bony landmarks to reliably detect the cervical segmental levels in vivo.
Presence of Human Enteric Viruses in the Stools of Healthy Malawian 6‐Month‐Old Infants
Authors: Rodríguez‐Díaz Jesús , Mira‐Pascual Laia , Collado Maria Carmen , Endo Akihito , Hyöty Heikki , Mangani Charles , Maleta Kenneth , Ashorn Per , Salminen Seppo
Published: October 2013

The acquisition of intestinal microbiota is essential for infants who are also in close contact with intestinal viruses. We assayed the presence of human enteric viruses in the faeces of 44 healthy breast‐fed 6‐month‐old infants from rural Malawi. Half of the infants tested harboured enteroviruses, although the infants had no gastric symptoms, suggesting a viral community mainly composed of human asymptomatic enteroviruses.
Vitellibacter soesokkakensis sp. nov., isolated from the junction between the ocean and a freshwater spring and emended description of the genus Vitellibacter
Authors: Park Sooyeon , Lee Ken-Chul , Bae Kyung Sook , Yoon Jung-Hoon
Published: October 2013

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated, motile by gliding and rod-shaped bacterial strain, RSSK-12T, was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain RSSK-12T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain RSSK-12T clustered with the type strains of two

Vitellibacter

species, with which it exhibited 94.8–96.9 % sequence similarity. Sequence similarities to the type strains of species of the genus

Aequorivita

and of other recognized species were 94.7–95.5 % and less than 91.9 %, respectively. Strain RSSK-12T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids of strain RSSK-12T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain RSSK-12T was 38.9 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, revealed that strain RSSK-12T is separate from other

Vitellibacter

species. On the basis of the data presented, strain RSSK-12T is considered to represent a novel species of the genus

Vitellibacter

, for which the name Vitellibacter soesokkakensis sp. nov. is proposed. The type strain is RSSK-12T ( = KCTC 32536T = CECT 8398T).
Glycogen synthase kinase 3 promotes p53 mRNA translation via phosphorylation of RNPC1
Authors: Zhang Min , Zhang Jin , Chen Xiangling , Cho Seong-Jun , Chen Xinbin
Published: October 2013

The RNPC1 RNA-binding protein, also called Rbm38, is a target of p53 and a repressor of p53 mRNA translation. Thus, the p53–RNPC1 loop is critical for modulating p53 tumor suppression, but it is not clear how the loop is regulated. Here, we showed that RNPC1 is phosphorylated at Ser195 by glycogen synthase kinase 3 (GSK3). We also showed that GSK3 promotes p53 mRNA translation through phosphorylation of RNPC1. Interestingly, we found that the phosphor-mimetic mutant S195D and the deletion mutant Δ189–204, which lacks the GSK3 phosphorylation site, are unable to repress p53 mRNA translation due to loss of interaction with eukaryotic translation factor eIF4E on p53 mRNA. Additionally, we found that phosphorylated RNPC1, RNPC1-S195D, and RNPC1(Δ189–204) promote p53 mRNA translation through interaction with eukaryotic translation factor eIF4G, which then facilitates the assembly of the eIF4F complex on p53 mRNA. Furthermore, we showed that upon inhibition of the phosphatidylinositol 3-kinase (PI3K)–Akt pathway, GSK3 is activated, leading to increased RNPC1 phosphorylation and increased p53 expression in a RNPC1-dependent manner. Together, we postulate that the p53–RNPC1 loop can be explored to increase or decrease p53 activity for cancer therapy.
RNF4 and PLK1 are required for replication fork collapse in ATR-deficient cells
Authors: Ragland Ryan L. , Patel Sima , Rivard Rebecca S. , Smith Kevin , Peters Ashley A. , Bielinsky Anja-Katrin , Brown Eric J.
Published: October 2013

The ATR–CHK1 axis stabilizes stalled replication forks and prevents their collapse into DNA double-strand breaks (DSBs). Here, we show that fork collapse in Atr-deleted cells is mediated through the combined effects the sumo targeted E3-ubiquitin ligase RNF4 and activation of the AURKA–PLK1 pathway. As indicated previously, Atr-deleted cells exhibited a decreased ability to restart DNA replication following fork stalling in comparison with control cells. However, suppression of RNF4, AURKA, or PLK1 returned the reinitiation of replication in Atr-deleted cells to near wild-type levels. In RNF4-depleted cells, this rescue directly correlated with the persistence of sumoylation of chromatin-bound factors. Notably, RNF4 repression substantially suppressed the accumulation of DSBs in ATR-deficient cells, and this decrease in breaks was enhanced by concomitant inhibition of PLK1. DSBs resulting from ATR inhibition were also observed to be dependent on the endonuclease scaffold protein SLX4, suggesting that RNF4 and PLK1 either help activate the SLX4 complex or make DNA replication fork structures accessible for subsequent SLX4-dependent cleavage. Thus, replication fork collapse following ATR inhibition is a multistep process that disrupts replisome function and permits cleavage of the replication fork.
The emerging role of the Nrf2–Keap1 signaling pathway in cancer
Authors: Jaramillo Melba C. , Zhang Donna D.
Published: October 2013

The Nrf2 (nuclear factor erythroid 2 [NF-E2]-related factor 2 [Nrf2])–Keap1 (Kelch-like erythroid cell-derived protein with CNC homology [ECH]-associated protein 1) signaling pathway is one of the most important cell defense and survival pathways. Nrf2 can protect cells and tissues from a variety of toxicants and carcinogens by increasing the expression of a number of cytoprotective genes. As a result, several Nrf2 activators are currently being tested as chemopreventive compounds in clinical trials. Just as Nrf2 protects normal cells, studies have shown that Nrf2 may also protect cancer cells from chemotherapeutic agents and facilitate cancer progression. Nrf2 is aberrantly accumulated in many types of cancer, and its expression is associated with a poor prognosis in patients. In addition, Nrf2 expression is induced during the course of drug resistance. Collectively, these studies suggest that Nrf2 contributes to both intrinsic and acquired chemoresistance. This discovery has opened up a broad spectrum of research geared toward a better understanding of the role of Nrf2 in cancer. This review provides an overview of (1) the Nrf2–Keap1 signaling pathway, (2) the dual role of Nrf2 in cancer, (3) the molecular basis of Nrf2 activation in cancer cells, and (4) the challenges in the development of Nrf2-based drugs for chemoprevention and chemotherapy.
Regulation of PCP by the Fat signaling pathway
Authors: Matis Maja , Axelrod Jeffrey D.
Published: October 2013

Planar cell polarity (PCP) in epithelia, orthogonal to the apical–basal axis, is essential for numerous developmental events and physiological functions. Drosophila model systems have been at the forefront of studies revealing insights into mechanisms regulating PCP and have revealed distinct signaling modules. One of these, involving the atypical cadherins Fat and Dachsous and the ectokinase Four-jointed, appears to link the direction of cell polarization to the tissue axes. We discuss models for the function of this signaling module as well as several unanswered questions that may guide future investigations.
Genome-wide high resolution parental-specific DNA and histone methylation maps uncover patterns of imprinting regulation in maize
Authors: Zhang Mei , Xie Shaojun , Dong Xiaomei , Zhao Xin , Zeng Biao , Chen Jian , Li Hui , Yang Weilong , Zhao Hainan , Wang Gaokui , Chen Zongliang , Sun Silong , Hauck Andrew , Jin Weiwei , Lai Jinsheng
Published: October 2013

Genetic imprinting is a specific epigenetic phenomenon in which a subset of genes is expressed depending on their parent-of-origin. Two types of chromatin modifications, DNA methylation and histone modification, are generally believed to be involved in the regulation of imprinting. However, the genome-wide correlation between allele-specific chromatin modifications and imprinted gene expression in maize remains elusive. Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. For DNA methylation, thousands of parent-of-origin dependent differentially methylated regions (pDMRs) were identified. All pDMRs were uniformly paternally hypermethylated and maternally hypomethylated. We also identified 1131 allele-specific H3K27me3 peaks that are preferentially present in the maternal alleles. Maternally expressed imprinted genes (MEGs) and paternally expressed imprinted genes (PEGs) had different patterns of allele-specific DNA methylation and H3K27me3. Allele-specific expression of MEGs was not directly related to allele-specific H3K27me3, and only a subset of MEGs was associated with maternal-specific DNA demethylation, which was primarily located in the upstream and 5′ portion of gene body regions. In contrast, allele-specific expression of a majority of PEGs was related to maternal-specific H3K27me3, with a subgroup of PEGs also associated with maternal-specific DNA demethylation. Both pDMRs and maternal H3K27me3 peaks associated with PEGs are enriched in gene body regions. Our results indicate highly complex patterns of regulation on genetic imprinting in maize endosperm.
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
Authors: Wu Chan-Shuo , Yu Chun-Ying , Chuang Ching-Yu , Hsiao Michael , Kao Cheng-Fu , Kuo Hung-Chih , Chuang Trees-Juen
Published: October 2013

Trans-splicing is a post-transcriptional event that joins exons from separate pre-mRNAs. Detection of trans-splicing is usually severely hampered by experimental artifacts and genetic rearrangements. Here, we develop a new computational pipeline, TSscan, which integrates different types of high-throughput long-/short-read transcriptome sequencing of different human embryonic stem cell (hESC) lines to effectively minimize false positives while detecting trans-splicing. Combining TSscan screening with multiple experimental validation steps revealed that most chimeric RNA products were platform-dependent experimental artifacts of RNA sequencing. We successfully identified and confirmed four trans-spliced RNAs, including the first reported trans-spliced large intergenic noncoding RNA (“tsRMST”). We showed that these trans-spliced RNAs were all highly expressed in human pluripotent stem cells and differentially expressed during hESC differentiation. Our results further indicated that tsRMST can contribute to pluripotency maintenance of hESCs by suppressing lineage-specific gene expression through the recruitment of NANOG and the PRC2 complex factor, SUZ12. Taken together, our findings provide important insights into the role of trans-splicing in pluripotency maintenance of hESCs and help to facilitate future studies into trans-splicing, opening up this important but understudied class of post-transcriptional events for comprehensive characterization.
Sparing of spatial mental imagery in patients with hippocampal lesions
Authors: Kim Soyun , Borst Grégoire , Thompson William L. , Hopkins Ramona O. , Kosslyn Stephen M. , Squire Larry R.
Published: October 2013

In four experiments, we explored the capacity for spatial mental imagery in patients with hippocampal lesions, using tasks that minimized the role of learning and memory. On all four tasks, patients with hippocampal lesions performed as well as controls. Nonetheless, in separate tests, the patients were impaired at remembering the materials that had been used to assess mental imagery. The findings suggest that the hippocampus is not needed for constructing many forms of spatial imagery but is needed for the formation of long-term memory. In future studies of the neural organization of spatial mental imagery, it will be important to separate the contribution of spatial processing from the contribution of learning and memory.
Preparation and structural analysis of (±)-threo-ritalinic acid
Authors: Wyss Sara , Werner Irmgard A. , Schweizer W. Bernd , Ametamey Simon M. , Milicevic Sephton Selena
Published: October 2013

Hydrolysis of the methyl ester (±)-threo-methyl phenidate afforded the free acid in 40% yield,viz.(±)-threo-ritalinic acid, C13H17NO2. Hydrolysis and subsequent crystallization were accomplished at pH values between 5 and 7 to yield colourless prisms which were analysed by X-ray crystallography. Crystals of (±)-threo-ritalinic acid belong to theP21/nspace group and form intermolecular hydrogen bonds. An antiperiplanar disposition of the H atoms of the (HOOC—)CH—CHpygroup (py is pyridine) was found in both the solid (diffraction analysis) and solution state (NMR analysis). It was also determined that (±)-threo-ritalinic acid conforms to the minimization of negativegauche+–gauche−interactions.
Structures of cefradine dihydrate and cefaclor dihydrate from DFT-D calculations
Authors: van de Streek Jacco , Rantanen Jukka , Bond Andrew D.
Published: October 2013

The crystal structure of cefradine dihydrate, C16H19N3O4S·2H2O, is considered in the pharmaceutical sciences to be the epitome of an isolated-site hydrate. The structure from single-crystal X-ray data was described in 1976, but atomic coordinates were not published. The atomic coordinates are determined here by combining the information available from the published single-crystal data with a dispersion-corrected density functional theory (DFT-D) method that has been validated to reproduce molecular crystal structures very accurately. Additional proof for the correctness of the structure comes from comparison with cefaclor dihydrate, C15H14ClN3O4S·2H2O, which is isomorphous and for which more complete single-crystal data are available. H-atom positions have not previously been published for either compound. The DFT-D calculations confirm that both cefradine and cefaclor are present in the zwitterionic form in the two dihydrate structures. A potential ambiguity concerning the orientation of the cyclohexadienyl ring in cefradine dihydrate is also clarified, and on the basis of the calculated energies it is shown that disorder should not be expected at room temperature. The DFT-D methods can be applied to recover full structural data in cases where only partial information is available, and where it may not be possible or desirable to obtain new experimental data.
Molecular replacement then and now
Authors: Scapin Giovanna
Published: October 2013

The `phase problem' in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962),Acta Cryst.15, 24–31]. The term `molecular replacement' was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972),The Molecular Replacement Method.New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the `best' search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to ensure that their deposited structures, which are potential search probes for future systems, are of the best possible quality.
Applications of molecular replacement to G protein-coupled receptors
Authors: Kruse Andrew C. , Manglik Aashish , Kobilka Brian K. , Weis William I.
Published: October 2013

G protein-coupled receptors (GPCRs) are a large class of integral membrane proteins involved in regulating virtually every aspect of human physiology. Despite their profound importance in human health and disease, structural information regarding GPCRs has been extremely limited until recently. With the advent of a variety of new biochemical and crystallographic techniques, the structural biology of GPCRs has advanced rapidly, offering key molecular insights into GPCR activation and signal transduction. To date, almost all GPCR structures have been solved using molecular-replacement techniques. Here, the unique aspects of molecular replacement as applied to individual GPCRs and to signaling complexes of these important proteins are discussed.
Extending molecular-replacement solutions withSHELXE
Authors: Thorn Andrea , Sheldrick George M.
Published: October 2013

Although the programSHELXEwas originally intended for the experimental phasing of macromolecules, it can also prove useful for expanding a small protein fragment to an almost complete polyalanine trace of the structure, given a favourable combination of native data resolution (better than about 2.1 Å) and solvent content. A correlation coefficient (CC) of more than 25% between the native structure factors and those calculated from the polyalanine trace appears to be a reliable indicator of success and has already been exploited in a number of pipelines. Here, a more detailed account of this usage ofSHELXEfor molecular-replacement solutions is given.
1,5-Dimethoxynaphthalene
Authors: Marfo-Owusu Emmanuel , Thompson Amber L.
Published: October 2013

The title compound, C12H12O2, lies across an inversion centre. The molecular structure suggests that the methoxy groups in the 1- and 5-positions of the naphthalene moiety do not significantly distort the planar conformation of the ring system, which has a maximum deviation of 0.0025 (9) Å. In the crystal, molecules pack in a herringbone arrangement in layers parallel to (100) and with chains propagating along [101] formed by very weak C—H...O interactions.
(6S*)-6-[(1S*,2R*)-1,2-Dihydroxypentyl]-4-methoxy-5,6-dihydro-2H-pyran-2-one
Authors: Valenti Domenic J. , Arif Atta M. , Strobel Gary A. , Harper James K.
Published: October 2013

The title compound, C11H18O5, was isolated from a liquid culture ofPestalotiopsis sp. In the molecule, the pyran-2-one ring assumes a half-chair conformation. The two terminal C atoms of the pentyl group were refined as disordered over two sets of sites, with refined occupancies of 0.881 (10) and 0.119 (10). In the crystal, molecules are linkedviaO—H...O hydrogen bonds forming a three-dimensional network.
1,5-Bis(4-isopropylbenzylidene)thiocarbonohydrazide
Authors: Han Yan-Hua , Zhao Qiao , Wang Yong
Published: October 2013

The title compound, C21H26N4S, was synthesized by the condensation reaction of 4-isopropylbenzaldehyde with thiocarbohydrazide in ethanol. The planes of the two benzene rings in the molecule are inclined at 22.6 (1)°. In the crystal, pairs of intermolecular N—H...S hydrogen bonds link the molecules into inversion dimers.
Bis[4-(dimethylamino)pyridinium] tetrachloridocuprate(II)
Authors: Bouacida Sofiane , Bouchene Rafika , Khadri Amina , Belhouas Ratiba , Merazig Hocine
Published: October 2013

The asymmetric unit of the title salt, (C7H11N2)2[CuCl4], comprises half a tetrahedral tetrachloridocuprate anion, being located on a twofold axis, and a protonated 4-(dimethylamino)pyridine cation. The geometry around the CuIIion is highly distorted with the range of Cl—Cu—Cl angles being 94.94 (1)–141.03 (1)°. The crystal structure is stabilized by N—H...Cl and C—H...Cl hydrogen bonds. In the three-dimensional network, cations and anions pack in the lattice so as to generate chains of [CuCl4]2−anions separated by two orientations of cation layers, which are interlocked through π–π stacking contacts between pairs of pyridine rings, with centroid–centroid distances of 3.7874 (7) Å.
Methyl 2-[4-(trifluoromethyl)phenylsulfanyl]benzoate
Authors: Yamuna Thammarse S. , Jasinski Jerry P. , Anderson Brian J. , Yathirajan H. S. , Kaur Manpreet
Published: October 2013

In the title compound, C15H13F3O2S, the dihedral angle between the benzene rings is 79.5 (1)°. The ester group is twisted by 7.6 (1)° from the mean plane of the adjacent benzene ring. Disorder was modeled over two sites for one F atom of the trifluoromethyl group with an occupancy ratio of 0.54 (6):0.46 (6). In the crystal, molecules are linkedviaweak C—H...O hydrogen bonds, forming two-dimensional networks lying parallel to (101). The networks are linkedviaC—H...π interactions, leading to the formation of a three-dimensional supramolecular structure.
(2,2′-Bipyridine-κ2N,N′)bis(nitrato-κ2O,O′)copper(II)
Authors: Liu Feng-Yi , Zhang Ming-Hui , Kou Jun-Feng
Published: October 2013

In the title complex, [Cu(NO3)2(C10H8N2)], the CuIIcation is chelated by two nitrate anions and by one 2,2′-bipyridine ligand in a distorted N2O4octahedral geometry. The dihedral angle between the pyridine rings is 1.92 (11)°. In the crystal, π–π stacking between parallel pyridine rings of adjacent complex molecules is observed, the centroid–centroid distance being 3.6788 (19) Å. Weak C—H...O hydrogen bonds further link the molecules into a three-dimensional supramolecular architecture.
N-[5-(Diphenylphosphorylmethyl)-4-(4-fluorophenyl)-6-isopropylpyrimidin-2-yl]-N-methylmethanesulfonamide
Authors: Wu Ya-Ming
Published: October 2013

In the title compound, C28H29FN3O3PS, the pyrimidine ring is oriented at a dihedral angle of 50.9 (2)° with respect to the florobenzene ring, while the two phenyl rings bonding to the same P atom are twisted with respect to each other, making a dihedral angle of 62.2 (2)°. In the crystal, molecules are linked by weak C—H...O and C—H...F hydrogen bonds into a three-dimensional supramolecular architecture.
The governance dimension of human development
Authors: Gamlath Sharmila
Published: October 2013

Purpose

– The research aims to include good governance as a facet in the measurement of human development.

Design/methodology/approach

– A modified Human Development Index (MHDI) was computed by including a governance dimension computed using the six governance indicators published by the World Bank. The rankings using the new index were obtained and compared to the rankings of the United Nations Development Programme's (UNDP's) HDI.

Findings

– The rank correlation of the original and modified indices was very high, but there were many big rank changes for individual countries in each HDI group. These rank changes could be largely reconciled in the light of the rankings of these countries in the Corruption Perceptions Index and the Democracy Index.

Research limitations/implications

– The research considers the measurement of human development at a point in time alone and incorporates 2010 governance indicators into the 2011 HDI, which could lead to a discrepancy in time periods considered. Furthermore, the governance indicators are measures of perceptions which can be subjective. The Practical implications paper does not delve into the country-specific factors that may have caused big rank changes.

Practical implications

– The paper builds a case for incorporating, or at least providing the option of including a governance dimension in the HDI.

Originality/value

– The paper is a novel attempt to incorporate good governance as a dimension in the HDI. It reasserts the need for policy-makers and governments to realize that peoples' capabilities cannot be realized in the absence of good governance, and that whilst improving other facets of human development, much attention needs to be paid towards establishing good governance.
Social action theory for understanding information security non-compliance in hospitals
Authors: Hedström Karin , Karlsson Fredrik , Kolkowska Ella
Published: October 2013

Purpose

– Employees' compliance with information security policies is considered an essential component of information security management. The research aims to illustrate the usefulness of social action theory (SAT) for management of information security.

Design/methodology/approach

– This research was carried out as a longitudinal case study at a Swedish hospital. Data were collected using a combination of interviews, information security documents, and observations. Data were analysed using a combination of a value-based compliance model and the taxonomy laid out in SAT to determine user rationality.

Findings

– The paper argues that management of information security and design of countermeasures should be based on an understanding of users' rationale covering both intentional and unintentional non-compliance. The findings are presented in propositions with practical and theoretical implications: P1. Employees' non-compliance is predominantly based on means-end calculations and based on a practical rationality, P2. An information security investigation of employees' rationality should not be based on an a priori assumption about user intent, P3. Information security management and choice of countermeasures should be based on an understanding of the use rationale, and P4. Countermeasures should target intentional as well as unintentional non-compliance.

Originality/value

– This work is an extension of Hedström et al. arguing for the importance of addressing user rationale for successful management of information security. The presented propositions can form a basis for information security management, making the objectives underlying the study presented in Hedström et al. more clear.
A framework for teaching network security in academic environments
Authors: Papanikolaou Alexandros , Vlachos Vasileios , Venieris Andreas , Ilioudis Christos , Papapanagiotou Konstantinos , Stasinopoulos Anastasios
Published: October 2013

Purpose

– Teaching information systems security features some peculiarities, compared to other scientific fields, as the trainees have to design and protect systems against both known and unknown attacks. Moreover, the so far established stereotypes present the potential intruders as being ingenious and able to penetrate almost every system. The paper aims to discuss these issues.

Design/methodology/approach

– Within the scope of two different modules in higher education institutes, the students' involvement into practical pre-designed scenarios was attempted, in order for them to understand the way intruders think, the methodologies they follow and the liabilities one may face for the flawed security of network applications and/or the supporting infrastructure. For this reason, an educational software tool was developed (named “Hackademic Challenges”), which comprised a variety of realistic scenarios, where the student had to locate and exploit various vulnerabilities, in order to successfully complete the challenge. Evaluation of the developed tool was attempted through an online, anonymous questionnaire.

Findings

– The results show that the students embraced this approach and have benefited significantly from going through these exercises.

Originality/value

– The contribution consists of findings that may be useful to other instructors teaching similar subjects.
Regional innovation and performance
Authors: Prevezer Martha , Li Jian , Panzarasa Pietro
Published: October 2013

Purpose

– This paper aims to draw on a number of indicators of innovation to evaluate and compare two central regions – Hubei and Hunan – with three leading regions of China – Beijing, Shanghai and Guangdong.

Design/methodology/approach

– The paper focuses on absorptive capacity at the level of domestic regions of China, using data on R&D expenditures, human resources in higher education and in high-tech industries. The paper uses social network analysis to investigate innovation networks based on patents from the SIPO and USPTO.

Findings

– Results indicate that, in Hubei and Hunan, R&D expenditures do not translate into as many innovative outputs as in the coastal and Southern regions. Moreover, high-tech industries contribute towards a relatively low proportion of the regional outputs of Hubei and Hunan, where especially the electronics industry is very poorly represented. Findings also suggest that Hubei and Hunan have a relatively limited access to foreign technologies embedded in ties with international partners. By contrast, the more advanced three regions tend to develop collaborative activities across national boundaries to a higher extent than across regional boundaries.

Research limitations/implications

– The analysis of China's regional innovation system has implications for research on national innovation systems. Policy-makers can benefit from the comparative analysis of regions.

Originality/value

– The study is primarily exploratory, and the findings contribute to the literature and ongoing discussion on data sources and methods for the analysis of regional innovation.
Choice of export entry mode by developing economies SMEs
Authors: El-Gohary Hatem , Edwards David , Eid Riyad , Huang Juanling
Published: October 2013

Purpose

– The purpose of this paper is to add to the accumulative knowledge in the field through investigating the different factors affecting the choice of export entry mode by Egyptian SMEs. An organised examination of the literature related to export entry modes by SMEs is discussed to provide and develop a clear understanding about the different factors affecting the choice of export entry mode by Egyptian SMEs. Such investigation will help in achieving a deep and reflective understanding of current exporting practises by Egyptian SMEs. The findings indicated that there is very few research studies in the literature related to the choice of export entry mode in developing countries in general and there was no published studies related to the choice of export entry mode in Egypt.

Design/methodology/approach

– The paper reviews the published literature related to choice of export entry mode by SMEs in general and to SMEs in developing countries (e.g. Egypt) in particular. Based on this review and the results of two focus groups, the paper validates a conceptual model utilising a positivist research philosophy with a quantitative approach, in which quantitative data are collected based on survey strategy through questionnaires to address different levels of the study.

Findings

– The findings showed that Egyptian SMEs owners, marketing and sales managers have a limited knowledge in relation to the different available export entry modes. The findings also illustrated that SME internal factors, local market factors and target market factors have different impacts on the choice of export entry mode and that only small number of Egyptian SMEs conducted an effective and efficient export activities.

Research limitations/implications

– The paper will provide great benefits for entrepreneurs, policy makers, practitioners, researchers and educators though providing a clearer view and deep understanding for the issues related to different factors affecting the choice of export entry mode by Egyptian SMEs.

Originality/value

– The paper adds to the extremely limited number of empirical studies that has been conducted to investigate different factors affecting the choice of export entry mode by Egyptian and Developing Economies SMEs. Depending on this research, researchers and scholars in the field can have a clearer view to set their attitude towards suitable future research studies which in turn will contribute to the related accumulated knowledge in the field.