bluuebunny/crossref_metadata_2025 huggingface dataset:
Insights in the electronic structure and redox reaction energy in LiFePO4 battery material from an accurate Tran-Blaha modified Becke Johnson potential
Authors: B. Araujo Rafael , S. de Almeida J. , Ferreira da Silva A. , Ahuja Rajeev
Published: September 2015

The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO4 and FePO4 which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, that the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO4 and FePO4. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.
Electronic structure and photovoltaic application of BiI3
Authors: Lehner Anna J. , Wang Hengbin , Fabini Douglas H. , Liman Christopher D. , Hébert Claire-Alice , Perry Erin E. , Wang Ming , Bazan Guillermo C. , Chabinyc Michael L. , Seshadri Ram
Published: September 2015

Rapid recent improvement in photovoltaic efficiency in hybrid lead halide perovskite materials has provided the impetus for understanding other, related main-group halide systems. Here, we show that the closely related but less toxic bismuth iodide BiI3 can show promising optoelectronic properties. Layered binary BiI3 is used here as the active layer in planar solar cell architectures (efficiency approximately 0.3%). Experimental and computational studies of absolute band positions of BiI3 are also presented, to help in the rational design of device architectures that would allow efficient charge transfer at the interfaces.
Automatic slice-alignment method in cardiac magnetic resonance imaging for evaluation of the right ventricle in patients with pulmonary hypertension
Authors: Yokoyama Kenichi , Nitta Shuhei , Kuhara Shigehide , Ishimura Rieko , Kariyasu Toshiya , Imai Masamichi , Nitatori Toshiaki , Takeguchi Tomoyuki , Shiodera Taichiro
Published: September 2015

We propose a new automatic slice-alignment method, which enables right ventricular scan planning in addition to the left ventricular scan planning developed in our previous work, to simplify right ventricular cardiac scan planning and assess its accuracy and the clinical acceptability of the acquired imaging planes in the evaluation of patients with pulmonary hypertension. Steady-state free precession (SSFP) sequences covering the whole heart in the end-diastolic phase with ECG gating were used to acquire 2D axial multislice images. To realize right ventricular scan planning, two morphological feature points are added to be detected and a total of eight morphological features of the heart were extracted from these series of images, and six left ventricular planes and four right ventricular planes were calculated simultaneously based on the extracted features. The subjects were 33 patients (25 with chronic thromboembolic pulmonary hypertension and 8 with idiopathic pulmonary arterial hypertension). The four right ventricular reference planes including right ventricular short-axis, 4-chamber, 2-chamber, and 3-chamber images were evaluated. The acceptability of the acquired imaging planes was visually evaluated using a 4-point scale, and the angular differences between the results obtained by this method and by conventional manual annotation were measured for each view. The average visual scores were 3.9±0.4 for short-axis images, 3.8±0.4 for 4-chamber images, 3.8±0.4 for 2-chamber images, and 3.5±0.6 for 3-chamber images. The average angular differences were 8.7±5.3, 8.3±4.9, 8.1±4.8, and 7.9±5.3 degrees, respectively. The processing time was less than 2.5 seconds in all subjects. The proposed method, which enables right ventricular scan planning in addition to the left ventricular scan planning developed in our previous work, can provide clinically acceptable planes in a short time and is useful because special proficiency in performing cardiac MR for patients with right ventricles of various sizes and shapes is not required.
Asymmetric nanotopography biases cytoskeletal dynamics and promotes unidirectional cell guidance
Authors: Sun Xiaoyu , Driscoll Meghan K. , Guven Can , Das Satarupa , Parent Carole A. , Fourkas John T. , Losert Wolfgang
Published: September 2015

Significance

Directed motion of cells is essential to many natural and physiological processes, including development and wound healing. Although gradients in chemical or physical properties are well known to guide cells, gradients that are strong enough to guide cells can only cover limited distances. Here we demonstrate that materials with local asymmetries in nano/microtopography on subcellular scales are able to guide cells with a single preferred direction. Unlike conventional gradients, local asymmetries on subcellular scales can be repeated over arbitrarily large regions, providing directional guidance over an unlimited range. This unidirectional guidance is mediated by biasing of the direction of waves of polymerization of the cell’s actin scaffolding, a mechanism that is conserved from primitive cells to human cells.
Global transcriptional repression: An initial and essential step for
Plasmodium
sexual development
Authors: Yuda Masao , Iwanaga Shiroh , Kaneko Izumi , Kato Tomomi
Published: September 2015

Significance

In malaria parasites, gametocytogenesis is a process whereby gametocytes, the precursors of gametes, are generated from asexual blood-stage parasites. In this study, we report that the plasmodium transcriptional repressor AP2-G2 plays an essential role in this process. We found that AP2-G2 represses the genes that are required for the proliferation of the asexual stage and, thereby, supports the conversion from the asexual blood stage to the nonreplicative sexual stage. Similarly, during the initial phase of germ-line formation in metazoan animals (including insects), a master transcriptional repressor specifies primordial germ cells among embryonic cells. Thus, our findings suggest that the basic molecular mechanisms that are required to establish the germ line have been conserved in eukaryotes, despite their evolutionary divergence.
Placebo analgesia and its opioidergic regulation suggest that empathy for pain is grounded in self pain
Authors: Rütgen Markus , Seidel Eva-Maria , Silani Giorgia , Riečanský Igor , Hummer Allan , Windischberger Christian , Petrovic Predrag , Lamm Claus
Published: September 2015

Significance

Empathy is of major importance for everyday social interaction. Recent neuroscientific models suggest that pain empathy relies on the activation of brain areas that are also engaged during the first-hand experience of pain. These models rely on rather unspecific and correlational evidence. Here, we show that inducing pain analgesia also reduces pain empathy, and that this is associated with decreased activation of empathy-related brain areas. We then document that blocking placebo analgesia via an opioid antagonist also blocks placebo analgesia effects on pain empathy. This finding suggests that pain empathy is grounded in neural responses and neurotransmitter activity related to first-hand pain.
Topology-defined units in numerosity perception
Authors: He Lixia , Zhou Ke , Zhou Tiangang , He Sheng , Chen Lin
Published: September 2015

Significance

What is a number? The answer to this age-old and fundamental question of philosophy has increasingly benefited from recent scientific investigation using psychology and neuroscience. To verify the invariant nature of numerosity perception, we manipulated the numbers of items connected/enclosed in arbitrary and irregular forms while controlling for various low-level visual features in different tasks and across small and large numbers. Results were consistent with the topological account, namely that numbers were strongly influenced by topological invariants (connectivity and the inside/outside relationship): connecting/enclosing items led to robust numerosity underestimation, with the extent of underestimation increasing monotonically with the number of connected/enclosed items. Brain image results also provided evidence that numbers represented in the intraparietal sulcus were influenced by topology.
Ecosystem carbon stocks and sequestration potential of federal lands across the conterminous United States
Authors: Tan Zhengxi , Liu Shuguang , Sohl Terry L. , Wu Yiping , Young Claudia J.
Published: September 2015

Significance

There has been a critical knowledge gap for national biological C sequestration potential assessment due to a lack of relevant information about federal lands that cover nearly 30% of the whole US territory. Here, we present the results from a multimodel simulation approach and fill the current knowledge gap by revealing the C sequestration potential of federal lands across the conterminous United States and their contribution to the national ecosystem C budget through 2050. This kind of information can be a fundamental reference for federal agencies to develop long-term strategies for mitigating greenhouse gas (GHG) emissions and sustaining federal land resources.
Metabotropic glutamate receptor signaling is required for NMDA receptor-dependent ocular dominance plasticity and LTD in visual cortex
Authors: Sidorov Michael S. , Kaplan Eitan S. , Osterweil Emily K. , Lindemann Lothar , Bear Mark F.
Published: September 2015

Significance

Interruption of normal sensory experience during early postnatal life often causes a permanent loss of synaptic strength in the brain and consequent functional impairment. For example, temporary monocular deprivation causes long-term depression (LTD) of synapses in the visual cortex of mammals, along with a profound loss of vision. The mechanisms by which this synaptic plasticity occurs are only partially understood. Here we show that signaling via metabotropic glutamate receptor 5 during a critical period of postnatal development establishes the biochemical conditions that are permissive for activity-dependent sculpting of excitatory synapses via the mechanism of NMDA receptor-dependent LTD.
Generation of Th17 cells in response to intranasal infection requires TGF-β1 from dendritic cells and IL-6 from CD301b
+
dendritic cells
Authors: Linehan Jonathan L. , Dileepan Thamotharampillai , Kashem Sakeen W. , Kaplan Daniel H. , Cleary Patrick , Jenkins Marc K.
Published: September 2015

Significance

Naïve helper T cells can differentiate into several specialized subtypes that help other cells kill microbes. The processes that determine how the different T-cell subtypes form in the body are not understood. Here we identify a population of dendritic cells that is responsible for the formation of one helper T-cell type during nasal infection. These results extend knowledge about T-cell specification and could be applied to improve vaccines for nasal pathogens.
Adiponectin supplementation in pregnant mice prevents the adverse effects of maternal obesity on placental function and fetal growth
Authors: Aye Irving L. M. H. , Rosario Fredrick J. , Powell Theresa L. , Jansson Thomas
Published: September 2015

Significance

Obesity and metabolic syndrome may, in part, originate in fetal life. In particular, babies of mothers with obesity and/or gestational diabetes mellitus (GDM) are often large at birth and have increased adiposity, which predisposes them to the development of metabolic disease later in life. Maternal obesity and GDM are typically associated with low circulating levels of adiponectin (ADN), and we found that ADN supplementation to pregnant obese mice completely normalized the changes in placental function and prevented fetal overgrowth caused by maternal obesity. These findings suggest that strategies to increase ADN levels in maternal obesity and GDM may alleviate the adverse effects of these pregnancy complications on the fetus.
TMEM16F is required for phosphatidylserine exposure and microparticle release in activated mouse platelets
Authors: Fujii Toshihiro , Sakata Asuka , Nishimura Satoshi , Eto Koji , Nagata Shigekazu
Published: September 2015

Significance

In activated platelets, a scramblase(s) scrambles phospholipids at plasma membranes and exposes phosphatidylserine (PtdSer) to the surface. PtdSer on activated platelets serves as a scaffold for the tenase and prothrombinase complexes for blood coagulation. Among five transmembrane protein 16 (TMEM16) members that support Ca
2+
-dependent phospholipid scrambling, TMEM16F is highly expressed in mouse platelets, and is indispensable for activation-induced PtdSer exposure and microparticle shedding. Thus, the rate of platelet-induced thrombin generation is severely reduced by the
TMEM16F
deficiency. The role of TMEM16F in PtdSer exposure on aggregated platelets is also shown in vivo with laser-induced thrombus formation. The phenotypes of
TMEM16F
-null mice resemble those of patients with Scott syndrome, a mild bleeding disorder, indicating that these mice provide a good model for this disease.
Computational probing protein–protein interactions targeting small molecules
Authors: Wang Yong-Cui , Chen Shi-Long , Deng Nai-Yang , Wang Yong
Published: September 2015

Motivation: With the booming of interactome studies, a lot of interactions can be measured in a high throughput way and large scale datasets are available. It is becoming apparent that many different types of interactions can be potential drug targets. Compared with inhibition of a single protein, inhibition of protein–protein interaction (PPI) is promising to improve the specificity with fewer adverse side-effects. Also it greatly broadens the drug target search space, which makes the drug target discovery difficult. Computational methods are highly desired to efficiently provide candidates for further experiments and hold the promise to greatly accelerate the discovery of novel drug targets.

Results: Here, we propose a machine learning method to predict PPI targets in a genomic-wide scale. Specifically, we develop a computational method, named as PrePPItar, to Predict PPIs as drug targets by uncovering the potential associations between drugs and PPIs. First, we survey the databases and manually construct a gold-standard positive dataset for drug and PPI interactions. This effort leads to a dataset with 227 associations among 63 PPIs and 113 FDA-approved drugs and allows us to build models to learn the association rules from the data. Second, we characterize drugs by profiling in chemical structure, drug ATC-code annotation, and side-effect space and represent PPI similarity by a symmetrical S-kernel based on protein amino acid sequence. Then the drugs and PPIs are correlated by Kronecker product kernel. Finally, a support vector machine (SVM), is trained to predict novel associations between drugs and PPIs. We validate our PrePPItar method on the well-established gold-standard dataset by cross-validation. We find that all chemical structure, drug ATC-code, and side-effect information are predictive for PPI target. Moreover, we can increase the PPI target prediction coverage by integrating multiple data sources. Follow-up database search and pathway analysis indicate that our new predictions are worthy of future experimental validation.

Conclusion: In conclusion, PrePPItar can serve as a useful tool for PPI target discovery and provides a general heterogeneous data integrative framework.

Availability and implementation: PrePPItar is available at http://doc.aporc.org/wiki/PrePPItar.

Contact:  ycwang@nwipb.cas.cn or ywang@amss.ac.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Drug-set enrichment analysis: a novel tool to investigate drug mode of action
Authors: Napolitano Francesco , Sirci Francesco , Carrella Diego , di Bernardo Diego
Published: September 2015

Motivation: Automated screening approaches are able to rapidly identify a set of small molecules inducing a desired phenotype from large small-molecule libraries. However, the resulting set of candidate molecules is usually very diverse pharmacologically, thus little insight on the shared mechanism of action (MoA) underlying their efficacy can be gained.

Results: We introduce a computational method (Drug-Set Enrichment Analysis—DSEA) based on drug-induced gene expression profiles, which is able to identify the molecular pathways that are targeted by most of the drugs in the set. By diluting drug-specific effects unrelated to the phenotype of interest, DSEA is able to highlight phenotype-specific pathways, thus helping to formulate hypotheses on the MoA shared by the drugs in the set. We validated the method by analysing five different drug-sets related to well-known pharmacological classes. We then applied DSEA to identify the MoA shared by drugs known to be partially effective in rescuing mutant cystic fibrosis transmembrane conductance regulator (CFTR) gene function in Cystic Fibrosis.

Availability and implementation: The method is implemented as an online web tool publicly available at http://dsea.tigem.it.

Contact:  dibernardo@tigem.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
Cytoscape.js: a graph theory library for visualisation and analysis
Authors: Franz Max , Lopes Christian T. , Huck Gerardo , Dong Yue , Sumer Onur , Bader Gary D.
Published: September 2015

Summary: Cytoscape.js is an open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used in a headless manner, useful for graph operations on a server, such as Node.js.

Availability and implementation: Cytoscape.js is implemented in JavaScript. Documentation, downloads and source code are available at http://js.cytoscape.org.

Contact:  gary.bader@utoronto.ca
XPIWIT—an XML pipeline wrapper for the Insight Toolkit
Authors: Bartschat Andreas , Hübner Eduard , Reischl Markus , Mikut Ralf , Stegmaier Johannes
Published: September 2015

Summary: The Insight Toolkit offers plenty of features for multidimensional image analysis. Current implementations, however, often suffer either from a lack of flexibility due to hard-coded C++ pipelines for a certain task or by slow execution times, e.g. caused by inefficient implementations or multiple read/write operations for separate filter execution. We present an XML-based wrapper application for the Insight Toolkit that combines the performance of a pure C++ implementation with an easy-to-use graphical setup of dynamic image analysis pipelines. Created XML pipelines can be interpreted and executed by XPIWIT in console mode either locally or on large clusters. We successfully applied the software tool for the automated analysis of terabyte-scale, time-resolved 3D image data of zebrafish embryos.

Availability and implementation: XPIWIT is implemented in C++ using the Insight Toolkit and the Qt SDK. It has been successfully compiled and tested under Windows and Unix-based systems. Software and documentation are distributed under Apache 2.0 license and are publicly available for download at https://bitbucket.org/jstegmaier/xpiwit/downloads/.

Contact:  johannes.stegmaier@kit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Political Centralization and Government Accountability *
Authors: Boffa Federico , Piolatto Amedeo , Ponzetto Giacomo A. M.
Published: September 2015

This article explains why decentralization can undermine accountability and answers three questions: what determines if power should be centralized or decentralized when regions are heterogeneous? How many levels of government should there be? How should state borders be drawn? We develop a model of political agency in which voters differ in their ability to monitor rent-seeking politicians. We find that rent extraction is a decreasing and convex function of the share of informed voters, because voter information improves monitoring but also reduces the appeal of holding office. As a result, information heterogeneity pushes toward centralization to reduce rent extraction. Taste heterogeneity pulls instead toward decentralization to match local preferences. Our model thus implies that optimal borders should cluster by tastes but ensure diversity of information. We also find economies of scope in accountability that explain why multiplying government tiers harms efficiency. A single government in charge of many policies has better incentives than many special-purpose governments splitting its budget and responsibilities. Hence, a federal system is desirable only if information varies enough across regions.
Fiber-optic Monitoring of Spinal Cord Hemodynamics in Experimental Aortic Occlusion
Authors: Kogler Angela S. , Bilfinger Thomas V. , Galler Robert M. , Mesquita Rickson C. , Cutrone Michael , Schenkel Steven S. , Yodh Arjun G. , Floyd Thomas F.
Published: September 2015

AbstractAbstract

The fiber-optic probe can be placed percutaneously into the epidural space of anesthetized sheep. Changes in blood flow detected by the probe correlated with microsphere-detected changes in spinal cord blood flow during occlusion and deocclusion of the thoracic aorta. Changes in spinal cord blood flow detected by the fiber-optic probe were markedly more rapid in onset than functional changes detected by motor-evoked responses.

Supplemental Digital Content is available in the text.

Background

Spinal cord ischemia occurs frequently during thoracic aneurysm repair. Current methods based on electrophysiology techniques to detect ischemia are indirect, non-specific, and temporally slow. In this article, the authors report the testing of a spinal cord blood flow and oxygenation monitor, based on diffuse correlation and optical spectroscopies, during aortic occlusion in a sheep model.

Methods

Testing was carried out in 16 Dorset sheep. Sensitivity in detecting spinal cord blood flow and oxygenation changes during aortic occlusion, pharmacologically induced hypotension and hypertension, and physiologically induced hypoxia/hypercarbia was assessed. Accuracy of the diffuse correlation spectroscopy measurements was determined via comparison with microsphere blood flow measurements. Precision was assessed through repeated measurements in response to pharmacologic interventions.

Results

The fiber-optic probe can be placed percutaneously and is capable of continuously measuring spinal cord blood flow and oxygenation preoperatively, intraoperatively, and postoperatively. The device is sensitive to spinal cord blood flow and oxygenation changes associated with aortic occlusion, immediately detecting a decrease in blood flow (−65 ± 32%; n = 32) and blood oxygenation (−17 ± 13%, n = 11) in 100% of trials. Comparison of spinal cord blood flow measurements by the device with microsphere measurements led to a correlation of R
2 = 0.49, P < 0.01, and the within-sheep coefficient of variation was 9.69%. Finally, diffuse correlation spectroscopy is temporally more sensitive to ischemic interventions than motor-evoked potentials.

Conclusion

The first-generation spinal fiber-optic monitoring device offers a novel and potentially important step forward in the monitoring of spinal cord ischemia.
Pancreatitis Subtypes Survey in 852 Childhood‐Onset Systemic Lupus Erythematosus Patients
Authors: Marques Victor L.S. , Gormezano Natali W.S. , Bonfá Eloisa , Aikawa Nadia E. , Terreri Maria T. , Pereira Rosa M. , Magalhães Claudia S. , Guariento Andressa , Appenzeller Simone , Ferriani Virgínia P. , Barbosa Cássia M. , Ramos Valéria C. , Lotufo Simone , Silva Clovis A.
Published: September 2015

Objective:

Pancreatitis is a rare and a life‐threatening systemic lupus erythematosus (SLE) manifestation in childhood‐onset SLE (cSLE). The objective of this study was to systematically classify pancreatitis in cSLE according to the International Study Group of Pediatric Pancreatitis and determine the overall prevalence, clinical features, laboratory, and first episode outcomes.

Methods:

A multicenter cohort study in 10 pediatric rheumatology centers, including 852 patients with cSLE.

Results:

Pancreatitis was diagnosed in 22 of 852 (2.6%) patients with cSLE. It was classified as acute pancreatitis in 20 (91%), acute recurrent pancreatitis in 2 (9%), and none of them had chronic pancreatitis. None of them had gallstones, traumatic pancreatitis, or reported alcohol/tobacco use. The comparison of patients with pancreatitis (first episode) and without this complication revealed a shorter disease duration (1 [0–10] vs 4 [0–23] years, P < 0.0001) and higher median of Systemic Lupus Erythematosus Disease Activity Index 2000 (21 [0–41] vs 2 [0–45], P < 0.0001). The frequencies of fever (P < 0.0001), weight loss (P < 0.0001), serositis (P < 0.0001), nephritis (P < 0.0001), arterial hypertension (P < 0.0001), acute renal failure (P < 0.0001), macrophage activation syndrome (P < 0.0001), and death (P = 0.001) were also higher in patients with pancreatitis. The frequencies of intravenous methylprednisolone use (P < 0.0001) and the median of prednisone dose (55 [15–60] vs 11 [1–90] mg/day, P < 0.0001) were significantly higher in patients with pancreatitis. Of note, the 2 patients with acute recurrent pancreatitis had 2 episodes, with pain‐free interval of 1 and 4 years.

Conclusions:

This was the first study characterizing pancreatitis using the International Study Group of Pediatric Pancreatitis standardized definitions in patients with cSLE showing that the predominant form is acute pancreatitis seen in association with glucocorticoid treatment and active severe disease.
Mechanism-based sirtuin enzyme activation
Authors: Guan Xiangying , Upadhyay Alok , Munshi Sudipto , Chakrabarti Raj
Published: September 2015

Sirtuin enzymes are NAD+-dependent protein deacylases that play a central role in the regulation of healthspan and lifespan in organisms ranging from yeast to mammals. There is intense interest in the activation of the seven mammalian sirtuins (SIRT1-7) in order to extend mammalian healthspan and lifespan. However, there is currently no understanding of how to design sirtuin-activating compounds beyond allosteric activators of SIRT1-catalyzed reactions that are limited to particular substrates. Moreover, across all families of enzymes, only a dozen or so distinct classes of non-natural small molecule activators have been characterized, with only four known modes of activation among them. None of these modes of activation are based on the unique catalytic reaction mechanisms of the target enzymes. Here, we report a general mode of sirtuin activation that is distinct from the known modes of enzyme activation. Based on the conserved mechanism of sirtuin-catalyzed deacylation reactions, we establish biophysical properties of small molecule modulators that can in principle result in enzyme activation for diverse sirtuins and substrates. Building upon this framework, we propose strategies for the identification, characterization and evolution of hits for mechanism-based enzyme activating compounds. We characterize several small molecules reported in the literature to activate sirtuins besides SIRT1, using a variety of biochemical and biophysical techniques including label-free and labeled kinetic and thermodynamic assays with multiple substrates and protocols for the identification of false positives. We provide evidence indicating that several of these small molecules reported in the published literature are false positives, and identify others as hit compounds for the design of compounds that can activate sirtuins through the proposed mechanism-based mode of action.
Investigation of the cellular reprogramming phenomenon referred to as stimulus-triggered acquisition of pluripotency (STAP)
Authors: Niwa Hitoshi
Published: September 2015

In 2014, it was reported that strong external stimuli, such as a transient low-pH stressor, was capable of inducing the reprogramming of mammalian somatic cells, resulting in the generation of pluripotent cells (Obokata et al. 2014a, b). This cellular reprograming event was designated ‘stimulus-triggered acquisition of pluripotency’ (STAP) by the authors of these reports. However, after multiple instances of scientific misconduct in the handling and presentation of the data were brought to light, both reports were retracted. To investigate the actual scientific significance of the purported STAP phenomenon, we sought to repeat the original experiments based on the methods presented in the retracted manuscripts and other relevant information. As a result, we have confirmed that the STAP phenomenon as described in the original studies is not reproducible.
Structure of RC1339/APRc fromRickettsia conorii, a retropepsin-like aspartic protease
Authors: Li Mi , Gustchina Alla , Cruz Rui , Simões Marisa , Curto Pedro , Martinez Juan , Faro Carlos , Simões Isaura , Wlodawer Alexander
Published: September 2015

The crystal structures of two constructs of RC1339/APRc fromRickettsia conorii, consisting of either residues 105–231 or 110–231 followed by a His tag, have been determined in three different crystal forms. As predicted, the fold of a monomer of APRc resembles one-half of the mandatory homodimer of retroviral pepsin-like aspartic proteases (retropepsins), but the quaternary structure of the dimer of APRc differs from that of the canonical retropepsins. The observed dimer is most likely an artifact of the expression and/or crystallization conditions since it cannot support the previously reported enzymatic activity of this bacterial aspartic protease. However, the fold of the core of each monomer is very closely related to the fold of retropepsins from a variety of retroviruses and to a single domain of pepsin-like eukaryotic enzymes, and may represent a putative common ancestor of monomeric and dimeric aspartic proteases.
Structure determination of uracil-DNAN-glycosylase fromDeinococcus radioduransin complex with DNA
Authors: Pedersen Hege Lynum , Johnson Kenneth A. , McVey Colin E. , Leiros Ingar , Moe Elin
Published: September 2015

Uracil-DNAN-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacteriumDeinococcus radiodurans(DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity betweenDrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme–DNA interaction. The complex revealed that the interaction betweenDrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphauget al.(1996).Nature (London),384, 87–92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) inDrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency ofDrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues in the N-terminus of a symmetry-related molecule and the complementary DNA strand facing away from the active site were also observed which seem to stabilize the enzyme–DNA complex. However, the significance of this observation remains to be investigated. The results provide new insights into the current knowledge about DNA damage recognition and repair by uracil-DNA glycosylases.
Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano–halogen interactions
Authors: Kamal Kulsoom , Maurya Hardesh K. , Gupta Atul , Vasudev Prema G.
Published: September 2015

The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano–halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013).RSC Adv.3, 12955–12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C—H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic–aromatic interactions and cyano–halogen interactions, further stabilizing the molecular packing. A database analysis of cyano–halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014).Angew. Chem. Int. Ed.53, 662–671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano–halogen interactions in their packing. Three geometric parameters for the C—X...N[triple-bond]C interaction (X = F, Cl, Br or I),viz.the N...Xdistance and the C—X...N and C—N...Xangles, were analysed. The results indicate that all the short cyano–halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.
5-Iodouracil: structure of a reflection twin
Authors: Lutz Martin , Klein Thomas J. S. de , Huijben Jeroen
Published: September 2015

The crystal structure of 5-iodouracil, C4H3IN2O2, has been determined in the noncentrosymmetric space groupP21on a nonmerohedrally twinned crystal. Both twin components are enantiomorphically pure, but the twin element is a mirror plane perpendicular toc*. The molecular structure is discussed and stacking faults in the two-dimensional packing are proposed as a reason for the twinning.
Methods of space-group determination – a supplement dealing with twinned crystals and metric specialization
Authors: Flack Howard D.
Published: September 2015

Tables for the determination of space group for single crystals, twinned crystals and crystals with a specialized metric are presented in the form of a spreadsheet for use on a computer. There are 14 tables, one for each of the Bravais-lattice types. The content of the tables is arranged so that at the intersection of rows, displaying the conditions for reflection, and of columns, displaying the Laue and crystal classes, one finds those space groups compatible with the observed Bravais-lattice type, the conditions for reflection and the Laue and crystal classes. The tables are intended to be of direct use to an experimentalist working with an unknown structure.
Crystal structure of [5-bromo-2-(pyridin-2-yl-κN)phenyl-κC1](pentane-2,4-dionato-κ2O,O′)platinum(II)
Authors: Fukuda Keito , Sugaya Tomoaki , Ishihara Koji
Published: September 2015

The title cyclometalated platinum(II) complex with 2-(4-bromophenyl)pyridinato and acetylacetonato ligands, [Pt(C11H7BrN)(C5H7O2)], consists of two crystallographically non-equivalent dimers, each stacked by π–π interactions with distances of ≃ 3.4 Å. In both dimers, the platinum(II) complexes are arranged antiparallel to each other. Each complex exhibits a slightly distorted square-planar coordination environment around the central Pt(II) atom. The dihedral angles between two chelate rings including the PtIIatom in these complexes are 0.08 (12) and 1.54 (9)°.
Crystal structure of (E)-4-[N-(7-methyl-2-phenylimidazo[1,2-a]pyridin-3-yl)carboximidoyl]phenol
Authors: Elaatiaoui Abdelmalik , Saddik Rafik , Benchat Noureddine , Saadi Mohamed , El Ammari Lahcen
Published: September 2015

The molecule of the title compound, C21H17N3O, is built up from fused five- and six-membered rings connected to a methyl group, a phenyl ring and an (iminomethyl)phenol group. The fused ring system is almost planar (r.m.s. deviation = 0.031 Å) and forms dihedral angles of 64.97 (7) and 18.52 (6)° with the phenyl ring and the (iminomethyl)phenol group, respectively. In the crystal, centrosymmetric molecules are linked by pairs of C—H...π interactions into dimeric units, which are further connected by O–H...N hydrogen bonds to form layers parallel to (101).
Soft-systems approaches to knowledge-cum-values management as innovation drivers
Authors: Zlatanović Dejana , Mulej Matjaž
Published: September 2015

Purpose

– Respecting the growing importance of interdependence of knowledge, values and social responsibility, the purpose of this paper is to introduce the concept of knowledge-cum-values management and to show how some soft systems approaches can support interdependence of knowledge and human values resulting in socially responsible innovative behavior, hence in success.

Design/methodology/approach

– The selected soft systems approaches are used to double-check the usefulness of the requisitely holistic approach to knowledge-cum-values management and innovation. The applied methodology for qualitative analysis is the Dialectical Systems Theory.

Findings

– One-sidedness, unlike the requisite holism, causes oversights and hence disables innovations as a new users’ benefit. Requisitely holistic knowledge-cum-values management prevents one-sidedness and therefore many oversights; hence it is a valuable driver of innovation. It is supported by social responsibility (exposing the systemic behavior by suggesting interdependence and holistic approach to one’s responsibility for one’s influences on society). By including values and by enabling consideration of interdependence of human values and knowledge, some soft systems approaches support innovative behavior with social responsibility.

Research limitations/implications

– Research is limited to theoretical findings resulting from authors’ previous empirical studies. The novel concept “knowledge-cum-values” erases the human dangerous one-sidedness resulting from the irrational rationalistic division of the two. Social responsibility supports informal use of some soft systems theories and diminishes this danger.

Practical implications

– The practical application of the selected soft systems approaches and social responsibility offers great possibilities for managers to improve the holism of their innovation processes, driven by knowledge-cum-values management. Fewer oversights are possible and lead to fewer mistakes and more success in the invention-innovation-diffusion processes. No human is rational or emotional only, either as a creator or as a consumer, but this fact is disregarded in the management literature.

Social implications

– Social responsibility shall be considered as an important novel soft-system approach and part of organizational innovative behavior aimed to replace the one-sided approaches prevailing so far and causing crises: the overseen attributes do not cease, but they still impact life and are out of control.

Originality/value

– The contribution introduces the new, still insufficiently researched concept of knowledge-cum-values management; it highlights new ways of attaining the requisitely holistic knowledge-cum-values management that enhances enterprise’s innovation capacity by requisite holism, supported by social responsibility.
Organizational leadership capability – a mechanism of knowledge coordination for inducing innovative behaviour
Authors: Kivipõld Kurmet
Published: September 2015

Purpose

– The purpose of this paper is to explore how organizational leadership capability as a knowledge coordinating mechanism affects service organization activities towards different stakeholder groups.

Design/methodology/approach

– The subjects in the case study are four Estonian service companies from the banking and retail industry providing high- and low-skill services, respectively. The data for the study were collected using the Organizational Leadership Capability Questionnaire with a total of 375 employees as respondents, and the organizations’ web sites to analyse corporate social responsibility (CSR). Assessment and analysis of the data included: the measurement of organizational leadership capability; the measurement of CSR communication; and analysis of the results gained from studying issues pertaining to organizational leadership capability as a knowledge coordination mechanism and innovative behaviour in terms of CSR.

Findings

– Ultimately, the study reveals that organizations with higher intensity of knowledge use in high-skill service industries have greater ability to coordinate knowledge as expressed in terms of organizational leadership capability, which in turn, allows them to behave more innovatively in terms of CSR towards stakeholders.

Research limitations/implications

– This study suggests that innovative behaviour in organizations towards different groups of stakeholders depends on organizational leadership capability. However, the results of this study are only valid in the context of the Estonia service sector, and more precisely the retail and banking industry.

Originality/value

– This paper demonstrates the role of organizational leadership capability in the coordination of knowledge to generate innovative behaviour in terms of CSR in service organizations.
The role of servicescape and image perceptions of customers on behavioral intentions in the hotel industry
Authors: Durna Ufuk , Dedeoglu Bekir Bora , Balikçioglu Sevgi
Published: September 2015

Purpose

– The purpose of this study is to examine the relationships between servicescape components, image and behavioral intentions within the framework of hotel businesses.

Design/methodology/approach

– Relationships between specified variables were tested with structural equation modeling (SEM) using a sample of 410 hotel customers.

Findings

– It was found that servicescape components had a positive effect on overall image, and overall image had the same effect on word-of-mouth (WOM) and re-visiting. It was also determined that overall image played a mediating role between servicescape and behavioral intention components. Overall, image played a partial mediating role between substantive staging of servicescape (SSoS) and WOM and a full mediating role among the other variables.

Practical implications

– For a business to maintain a positive image perception, servicescape components must be positively perceived, as well. Therefore, managers who intend to present a positive business image should design servicescape components according to current trends or the fashion expectations of target consumers. This would by default increase the attractiveness of the business. Moreover, businesses can create unique concepts by designing and developing new servicescape components. This step can be beneficial, especially for hotel businesses wishing to establish a specific brand. In this regard, it is recommended that businesses employ an expert who can track and organize servicescape developments.

Originality/value

– Although it has been found that there are specific relationships between servicescape, image and behavioral intentions, there has been a deficiency of empirical studies carried out within hotel industries. Furthermore, while SSoS has been investigated in the literature, communicative staging of servicescape (CSoS) has been neglected. In this regard, investigating the aforementioned relationships within the framework of the hotel industry contributes to the literature. Furthermore, in this study, an attempt has been made to stress the importance of servicescape, which is found to be essential for positive business image perception.
Investigating relationships between internal marketing practices and employee organizational commitment in the foodservice industry
Authors: Joung Hyun-Woo , Goh Ben K. , Huffman Lynn , Yuan Jingxue Jessica , Surles James
Published: September 2015

Purpose

– The purpose of this study is to investigate the relationships between internal marketing practices, employee job satisfaction, organizational commitment and turnover intention in the foodservice industry.

Design/methodology/approach

– The target population was employees who were currently working at a restaurant in the USA. All respondents were recruited from different states for the generalization of the study results. A confirmatory factor analysis validated the measurement model, and subsequently, structural equation modeling tested the proposed model.

Findings

– Three internal marketing practices – vision, development and rewards – were good indicators for predicting employee job satisfaction, and two internal marketing practices – development and rewards – in addition to job satisfaction were significant predictors for employee organizational commitment. Finally, the findings indicated that job satisfaction and affective commitment had a significant impact on lowering employee turnover intention.

Research limitations/implications

– In further research, more internal marketing practices – such as employee motivation, customer orientation, sharing information, employee empowerment – can be added to the model to increase employee job satisfaction and organizational commitment.

Practical implications

– Foodservice operators should focus on internal marketing practices to have satisfied employees who, in turn, are more likely to deliver high service quality to customers.

Originality/value

– This study has not only extended the influential scope of the internal marketing theory to organizational commitment, but has also proposed the antecedents of organizational commitment (i.e. internal marketing practices and employee job satisfaction) and clarified the relationships among them.