bluuebunny/crossref_metadata_2025 huggingface dataset:
Yield and water-use efficiency of wheat in a high-rainfall environment
Authors: Acuña Tina Botwright , Lisson Shaun , Johnson Peter , Dean Geoff
Published: April 2015

Yield, water use and water-use efficiency (WUE) in the high-rainfall zone of Tasmania are highly variable because of environmental and agronomic constraints to grain production that limit yield potential. The expansion of irrigation infrastructure in Tasmanian production systems with access to low-cost, plentiful irrigation sources will also influence these components in some areas. This paper reports on desktop modelling studies that aimed to benchmark wheat WUE and to explore the sensitivity of yield, water use and WUE to changes in management practice in a high-rainfall environment. Here, WUE was defined as: grain yield/(evapotranspiration + drainage + runoff). The crop simulation model APSIM-Wheat was used to quantify key water balance elements and estimate ‘attainable’ and ‘potential’ WUE and grain yield for 27 wheat trials. The upper limit for WUE was ~30 kg/ha.mm in excess of 180 mm evaporation, which is 16% higher than previous estimates at this southerly latitude for wheat. Attainable WUE ranged from 58% to 100% of potential WUE and was limited by nitrogen supply and water loss through evaporation, drainage and runoff. Model scenarios showed that co-limitation of inputs of nitrogen and irrigation was an important driver of grain yield and WUE. The implications of this research on crop management and production in temperate, high-rainfall environments are discussed.
Neurosyphilis and the impact of HIV infection
Authors: Ho Emily L. , Spudich Serena S.
Published: April 2015

Neurosyphilis is a complication of systemic syphilis. This review of the clinical presentation, diagnostic laboratory findings, treatment and management of neurosyphilis discusses the impact of HIV and the specific challenges it brings, focusing on areas of controversy, and highlighting important questions that remain to be answered.
Syphilis: a fresh look at an old foe
Authors: Chen Marcus Y. , Klausner Jeffrey D. , Fairley Christopher Kit , Guy Rebecca , Wilson David , Donovan Basil
Published: April 2015

Syphilis remains a pressing public health problem globally across different populations including men who have sex with men and pregnant women. It is timely to review what international surveillance data tell us and the evidence behind public health interventions aimed at controlling syphilis. A reinvigorated response to the re-emergence of syphilis is required.
Aftershock Triggers Augmented Pressor Effects in Survivors: Follow-Up of the Great East Japan Earthquake
Authors: Nishizawa Masafumi , Hoshide Satoshi , Okawara Yukie , Shimpo Masahisa , Matsuo Takefumi , Kario Kazuomi
Published: April 2015

BACKGROUND

Previous reports focused on the significant acute effects immediately after an earthquake on an increase in blood pressure (BP) assessed by ambulatory BP monitoring. However, there have been no data on the impact of environmental triggers on the long-term response to earthquake.

METHODS

We analyzed the ambulatory BP monitoring data of 8 patients who lived in the disaster area of the 11 March 2011 Great East Japan Earthquake on the day of the largest aftershock with a first tsunami warming (sirens) on 7 December 2012.

RESULTS

There was no significant difference in the BP in either the period 1 hour before (median (range): 126.5 (121.5–138.0) vs. 137.8 (129.5–177.0) mm Hg, P = 0.07) or that 1 hour after (139.3 (113.0–143.5) vs. 137.5 (125.0–192.0) mm Hg, P = 0.27) the aftershock between those living at home and those who had been living in temporary housing. After the time of aftershock, the systolic BP levels at that night (124.9 (113.2–137.9) vs. 107.0 (101.9–110.1) mm Hg, P = 0.021) and systolic BP levels at the following morning (149.3 (131.0–196.2) vs. 129.5 (128.8–131.0) mm Hg, P = 0.029) were also significantly higher in those living in temporary housing at the time compared to those living in their own homes.

CONCLUSION

Our data suggest that the stress of a change in living conditions following the disaster might have contributed an increased risk of cardiovascular events.
ScaffMatch: scaffolding algorithm based on maximum weight matching
Authors: Mandric Igor , Zelikovsky Alex
Published: April 2015

Motivation: Next-generation high-throughput sequencing has become a state-of-the-art technique in genome assembly. Scaffolding is one of the main stages of the assembly pipeline. During this stage, contigs assembled from the paired-end reads are merged into bigger chains called scaffolds. Because of a high level of statistical noise, chimeric reads, and genome repeats the problem of scaffolding is a challenging task. Current scaffolding software packages widely vary in their quality and are highly dependent on the read data quality and genome complexity. There are no clear winners and multiple opportunities for further improvements of the tools still exist.

Results: This article presents an efficient scaffolding algorithm ScaffMatch that is able to handle reads with both short (<600 bp) and long (>35 000 bp) insert sizes producing high-quality scaffolds. We evaluate our scaffolding tool with the F score and other metrics (N50, corrected N50) on eight datasets comparing it with the most available packages. Our experiments show that ScaffMatch is the tool of preference for the most datasets.

Availability and implementation: The source code is available at http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch.

Contact:  mandric@cs.gsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Definition and assessment of chronic pain in advanced disease
Authors: Rayment Clare , Bennett Michael I.
Published: April 2015

This chapter discusses the various definitions applied to pain including chronic, nociceptive, neuropathic, and breakthrough. It gives a broad overview of the epidemiology of pain including its prevalence of greater than 50% in those patients with advanced disease and its under-treatment. The second part of the chapter explains how best to characterize the pain complaint. It acknowledges the importance of a thorough history, including pain characteristics such as severity and associated features. Several pain measurement scales, which can be used both in clinical practice and research, are presented. Clinical examination and imaging are also discussed as aids to diagnosis and management of pain. It concludes with how to assess pain in the context of a palliative plan of care, stressing the need to consider the many challenges that patients face with advancing disease and how the management of pain is affected by other symptoms patients may have.
Bowel obstruction
Authors: Ripamonti Carla I. , Easson Alexandra M. , Gerdes Hans
Published: April 2015

In this chapter, malignant bowel obstruction is defined as the clinical presentation of patients with symptoms, signs, and radiographic evidence of obstruction to the transit of gastrointestinal contents caused by cancer, or the consequences of anticancer therapy including surgery, chemotherapy, or radiation therapy. Malignant bowel obstruction secondary to cancer or its treatments is encountered relatively frequently in supportive care as well as in in hospice/palliative care practice, carries a poor prognosis, and is associated with significant symptoms. Careful clinical assessment and an understanding of the patient’s disease trajectory are crucial in recommending the best way of providing palliation. In someone with a single-level obstruction and good functional status, surgery should be offered. Those with multilevel obstruction are almost never surgical candidates and should be managed with changes in oral intake and medications.
Aetiology, classification, assessment, and treatment of the anorexia-cachexia syndrome
Authors: Baracos Vickie E. , Watanabe Sharon M. , Fearon Kenneth C. H.
Published: April 2015

Anorexia-cachexia is a heterogeneous and multifactorial syndrome most likely driven by systemic inflammation and neuroendocrine activation. Key diagnostic features include reduced appetite, weight loss, and muscle wasting. Key clinical problems include management of anorexia without resort to artificial nutritional support, and muscle wasting that cannot be completely arrested/reversed even with such intervention. Assessment should cover domains such as body stores of energy and protein, food intake, performance status, and factors resulting in excess catabolism. Intervention should be early rather than late, informed by the assessment process and focused on a multimodal approach (nutrition, exercise, and pharmacological agents). This chapter aims to discuss these issues and provide (a) the reader with some background principles to classification, (b) a simple approach to patient assessment and a robust algorithm for basic multimodal treatment, and (c) an overview of the evidence base for different pharmacological interventions.
Speech and language therapy in palliative care
Authors: Luckett Tim , Reid Katherine L.P.
Published: April 2015

Palliative care is an emerging specialty within the field of speech and language therapy (SLT); the discipline is currently under-represented both in specialist services and the research literature. This belies the fact that many patients in the palliative phase suffer problems with swallowing (dysphagia) and communication, the core domains of SLT practice. This chapter provides an overview of difficulties encountered in these domains by people with life-limiting conditions together with common approaches to assessment and management. Assessment and management should be person-centred, integrated into multidisciplinary care, and seek to maintain function via minimal intervention for maximum gain. More research is needed to inform appropriately integrated, person-centred models of SLT provision that enable difficulties with communication and swallowing to be addressed alongside other symptoms and care needs. It seems likely that difficulties in these domains are currently under-identified and under-treated in many cases.
The applicability of motor learning to neurorehabilitation
Authors: Krakauer John W.
Published: April 2015

Rehabilitation is a form of directed training and is therefore predicated on the idea that patients respond to such training by learning. Current concepts in motor learning are reviewed. Recovery is not synonymous with re-learning and that it is important to be specific about what learning mechanism is being targeted by any given therapy. There is a unique milieu of heightened plasticity post-stroke that is responsible for reduction in impairment both through spontaneous biological recovery and increased responsiveness to training. In the chronic phase of stroke, plasticity returns to normal levels and learning for the most part only leads to task-specific compensation. Thus, new forms of intervention may have quite distinct effects depending on whether they are initiated in the sensitive period after stroke or in the chronic phase. It is to be hoped that new pharmacological and non-invasive brain stimulation approaches will allow the post-stroke sensitive period to be augmented, extended, and re-opened.
Virtual reality for neurorehabilitation
Authors: Riener Robert
Published: April 2015

Virtual reality (VR) is a powerful tool to motivate its participants to active participation, while providing augmented feedback to instruct the subject and improve task performance. This chapter presents the technical prerequisites of different recording, display, and rendering technologies. VR does not replace the real environment, but is a tool for setting up automatic training schedules. VR can be a good solution to train dangerous or difficult tasks. VR is being applied in physiotherapy, occupational therapy to recover limb functionality after disease or accident, and to enhance cognitive learning. VR technologies can also be applied to provide feedback as assistance during activities of daily living. Despite the many technological achievements and positive results in many therapeutic and assistive applications, the field of VR rehabilitation is still in an early phase. VR technologies will continue to grow, gain further mainstream acceptance and, eventually, have a significant positive effect on therapeutic outcome.
Neuroembryology and Congenital Malformations
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

More malformations occur in the nervous system than in any other organ system. Of the .05% of infants with major malformations, with roughly 60% of these major malformations affect the nervous system. The central nervous system is formed from ectodermal germinal cells which form the neuroblast> neuron; glioblast>astrocyte; and oligodendrocyte. Waves of neuronal migration form the central nervous system. The congenital malformations include abnormalities in growth and migration, chromosomal trisomy and translocation, defective fusion, and abnormalities in growth and in the ventricular system.
Functional Anatomy of the Brain Stem
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

The regions in the brain stem—medulla, pons, and midbrain—are reviewed. Each region is divided into a tectal (roof of ventricle), tegmental (floor of ventricle), and basilar zone (base of tegmentum). The major descending motor pathway controlling the brain stem, the corticonuclear tract, is described and its functions reviewed. Many of the major functional regions in the brain stem are reviewed: the reticular system, cardiovascular, deglutination, vomiting, emetic center, and coughing. There is also a guide included for localizing disease in the brain stem.
Motor Systems
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

The cerebellum forms the tectum of the medulla and pons and permits us to undertake fine movements smoothly. It is a laminated three-layer cortex with the principal cells, granule and Purkinje cells. There are three regions in the cerebellum: (1) floccular nodular lobe or archipallium, which receives direct vestibular input; (2) the paleocerebellum/anterior lobe, which receives the spinocerebellar and cuneocerebellar tracts, and the spino-olivary tracts; and (3) the neocerebellum/the middle and posterior lobes, which receive input from the neocortex via the middle cerebellar peduncle. Lesions in the cerebellum produce action tremors.
Somatosensory Function and the Parietal Lobe
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

The parietal lobe receives the major somatosensory systems via the projection from ventrobasal thalamic nuclei, which receive input from the ascending sensory systems: spinothalamic, medial lemniscus, and trigeminal lemniscus. The postcentral gyrus areas, 3-2-1, receive this direct thalamic input, which is organized in somatotopically and permits one to undertake discriminative sensory modalities. The superior parietal lobule is responsible for body image. The supramarginal and angular gyri of the inferior parietal lobule are involved with complex sensory dysfunctions.
Speech, Language, Cerebral Dominance, and the Aphasias
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

Most individuals are right handed (93%) and in those individuals the left-hemisphere is dominant for language. The lateral pulvinar nucleus of the thalamus is a multimodal somatic nucleus that is an important subcortical center which forms most of the projection on the inferior parietal lobule. There is anatomical asymmetry between the two hemispheres with the region behind Heschl’s gyrus in the left temporal lobe significantly larger and probably representing Wernicke’s speech area. Three areas in the dominant hemisphere are of major importance in language, Broca’s motor aphasia area in the opercular and triangular portions of the inferior frontal gyrus; Wernicke’s’ receptive aphasia area in the superior and lateral surface of the temporal lobe; and the angular and supramarginal region in the inferior parietal lobule with Gerstmann’s syndrome.
Cerebral Hemispheres
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

Ischemic occlusive diseases are caused by arteriosclerosis (15%), small vessel lacunae (9%), emboli (60%), dissections, and other causes (3%). The internal carotid may be involved by arteriosclerosis in its extracranial or intracranial portions. The most common site is the origin of the vessel at the bifurcation of the common carotid into the internal and external carotid. The middle cerebral artery is the direct continuation of the internal carotid artery, and it is a common site of syndromes either of the lenticulostriate branches or cortical branches. The anterior cerebral artery is a branch of the middle cerebral artery and is a less common site of disease. The posterior cerebral artery is the direct continuation of the vertebral basilar artery and symptoms in the brain stem and cerebellum are common from diseases in this artery.
Cerebral Hemispheres
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

Common causes of trauma to the brain result from accidents and in many cases not using a helmet or wearing a seat belt. These traumatic injuries can lead to extradural or subdural hematomas. Tumors/neoplasms are another nonvascular cause of disease in the brain. They are more common as one ages. Tumors may be intrinsic gliomas and metastatic. Extrinsic tumors are also common from meningiomas or metastatic lesions. Meningitis is the most common cause of infection to the nervous system and it can be caused by many organisms. Infections in the brain are also common sources of pathology in the brain following infections in the nasal sinuses, middle ear, or following compound skull fractures.
Learning, Memory, Amnesia, Dementia, Instinctive Behavior, and the Effects of Early Experience
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

Learning in humans is divided into two broad categories: declarative (explicit) or nondeclarative (reflexive). Declarative learning has an immediate or short-term working memory, a long-term labile stage, and then finally the long-term memory stage. Motivation influences our remembering. The hippocampus and entorhinal cortex of the hippocampus are the prime sites for new memories. There are many causes of memory disorders, including strokes, hypertension, alcoholism, drug overdoses, trauma, infection, and so on. Loss of neurons, and their dendritic spines, and the presence of neurofibrillar tangles are linked to the presence of dementia. Memory and learning disorders are common in the elderly with Alzheimer’s being a silent epidemic affecting over 5,000,000 elderly Americans and producing trauma to the entire family.
Case History Problem Solving
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

This chapter includes problem solving of general cases of the cerebral hemispheres with lesion diagrams and case histories
Case History Problem Solving
Authors: Marcus Elliott M. , Jacobson Stanley , Sabin Thomas D.
Published: April 2015

This chapter includes case history review and correlation to illustrations.
Artificial photosynthesis: understanding water splitting in nature
Authors: Cox Nicholas , Pantazis Dimitrios A. , Neese Frank , Lubitz Wolfgang
Published: April 2015

In the context of a global artificial photosynthesis (GAP) project, we review our current work on nature's water splitting catalyst. In a recent report (Coxet al. 2014Science345, 804–808 (doi:10.1126/science.1254910)), we showed that the catalyst—a Mn4O5Ca cofactor—converts into an ‘activated’ form immediately prior to the O–O bond formation step. This activated state, which represents an all MnIVcomplex, is similar to the structure observed by X-ray crystallography but requires the coordination of an additional water molecule. Such a structure locates two oxygens, both derived from water, in close proximity, which probably come together to form the product O2molecule. We speculate that formation of the activated catalyst state requires inherent structural flexibility. These features represent new design criteria for the development of biomimetic and bioinspired model systems for water splitting catalysts using first-row transition metals with the aim of delivering globally deployable artificial photosynthesis technologies.
Mangrovibacter yixingensis sp. nov., isolated from farmland soil
Authors: Zhang Hao , Guo Su-hui , Sun Bin , Zhang Jing , Cheng Ming-gen , Li Qiang , Hong Qing , Huang Xing
Published: April 2015

A Gram-staining-negative, facultatively anaerobic, rod-shaped, nitrogen-fixing bacterial strain, designated TULL-AT, was isolated from a farmland soil sample in Yixing, China. The optimal conditions for growth were 30 °C, pH 7.0–8.0 and 0 % (w/v) NaCl. Q8 was the dominant respiratory quinone and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and aminophospholipid. Phylogenetic analysis of 16S rRNA gene sequences showed that strain TULL-AT was most closely related to Mangrovibacter plantisponsor MSSRF40T (99.6 %), followed by Salmonella enterica subsp. diarizonae DSM 14847T (96.8 %) and Cronobacter condimenti 1330T (96.8 %). Sequence analysis of the genes rpoB, gyrB and hsp60 revealed that those of strain TULL-AT also exhibit high sequence similarity with those of the species M. plantisponsor MSSRF40T (95.5, 94.1 and 93.4 %). The genomic DNA G+C content was 52 mol%. The major fatty acids of strain TULL-AT were C16 : 0, C16 : 1ω7c and/or C16 : 1ω6c, C18 : 1ω7c /C18 : 1ω6c, C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I and iso-C17 : 1 I and/or anteiso-C17 : 1 B. Strain TULL-AT showed low DNA–DNA relatedness with M. plantisponsor MSSRF40T (35.10 ± 1.41 %). Based on the multiple genotypic and phenotypic data, strain TULL-AT is considered to represent a novel species of the genus Mangrovibacter, for which the name Mangrovibacter yixingensis sp. nov. is proposed. The type strain is TULL-AT ( = ACCC 19709T = KCTC 42181T).
Structural and functional analysis of betaine aldehyde dehydrogenase fromStaphylococcus aureus
Authors: Halavaty Andrei S. , Rich Rebecca L. , Chen Chao , Joo Jeong Chan , Minasov George , Dubrovska Ievgeniia , Winsor James R. , Myszka David G. , Duban Mark , Shuvalova Ludmilla , Yakunin Alexander F. , Anderson Wayne F.
Published: April 2015

When exposed to high osmolarity, methicillin-resistantStaphylococcus aureus(MRSA) restores its growth and establishes a new steady state by accumulating the osmoprotectant metabolite betaine. Effective osmoregulation has also been implicated in the acquirement of a profound antibiotic resistance by MRSA. Betaine can be obtained from the bacterial habitat or produced intracellularly from cholineviathe toxic betaine aldehyde (BA) employing the choline dehydrogenase and betaine aldehyde dehydrogenase (BADH) enzymes. Here, it is shown that the putative betaine aldehyde dehydrogenase SACOL2628 from the early MRSA isolate COL (SaBADH) utilizes betaine aldehyde as the primary substrate and nicotinamide adenine dinucleotide (NAD+) as the cofactor. Surface plasmon resonance experiments revealed that the affinity of NAD+, NADH and BA forSaBADH is affected by temperature, pH and buffer composition. Five crystal structures of the wild type and three structures of the Gly234Ser mutant ofSaBADH in the apo and holo forms provide details of the molecular mechanisms of activity and substrate specificity/inhibition of this enzyme.
Using support vector machines to improve elemental ion identification in macromolecular crystal structures
Authors: Morshed Nader , Echols Nathaniel , Adams Paul D.
Published: April 2015

In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based ona prioriexpectations of the chemical environment and X-ray scattering.
Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams
Authors: Coquelle Nicolas , Brewster Aaron S. , Kapp Ulrike , Shilova Anastasya , Weinhausen Britta , Burghammer Manfred , Colletier Jacques-Philippe
Published: April 2015

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, namedNanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out usingCrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.
SynchWeb: a modern interface for ISPyB
Authors: Fisher S. J. , Levik K. E. , Williams M. A. , Ashton A. W. , McAuley K. E.
Published: April 2015

SynchWeb is a modern interface to the ISPyB database. It significantly simplifies sample registration and is targeted towards live data collection monitoring and remote access for macromolecular crystallography. It adds a variety of new features including project management, an integrated diffraction image viewer, and a map and model viewer, as well as displaying results from automated analysis pipelines. Virtually all aspects of an experiment can be monitored through the web browser and the success of each experiment can be evaluated.
Monolayer effect of a gemini surfactant with a rigid biphenyl spacer on its self-crystallization at the air/liquid interface
Authors: Chen Qibin , Yao Junyao , Hu Xin , Shen Jincheng , Sheng Yujie , Liu Honglai
Published: April 2015

A gemini surfactant with a biphenyl spacer can spontaneously generate crystals at the air/solution interface. X-ray crystallography reveals that surfactant molecules exhibit an almost fully extended conformation with interdigitating alkyl chains, together with an approximate co-planarity of two C—C—C planes in two alkyl chains of one gemini molecule, and a prominent dihedral angle between the benzene rings and C—C—C planes of the alkyl chains. Infrared reflection–absorption spectroscopy shows that the gemini surfactant was stretched at the air/water interface, with the hydrocarbon chains oriented at a tilt angle of ∼75° with respect to the surface normal. In particular, the biphenyl group is more or less perpendicular to the water surface, and the C—C—C plane of the alkyl chain tends to be parallel to the water surface. Both results point out a remarkable similarity in the molecular conformation between the crystal and the monolayer. Meanwhile, dynamic light scattering and transmission electron microscopy results indicate that the crystallization of such gemini surfactants at the interface is contrary to the crystallization behavior in the bulk phase, meaning that the surfactant solution can only form a supersaturated solution as it is cooled, though the crystallization temperature of 296 K is lower than the Krafft temperature (∼303 K). Therefore, our findings indicate that the Gibbs monolayer of the gemini surfactant plays a critical role in its interfacial crystallization. Additionally, multiple weak intermolecular interactions, involving van der Waals interaction, π–π stacking and cationic–π interactions, as well as the hydrophobic effect during the aggregation of the gemini molecule in solution, are responsible for the formation of the interfacial crystal.
Online_DPI: a web server to calculate the diffraction precision index for a protein structure
Authors: Kumar K. S. Dinesh , Gurusaran M. , Satheesh S. N. , Radha P. , Pavithra S. , Thulaa Tharshan K. P. S. , Helliwell John R. , Sekar K.
Published: April 2015

An online computing server, Online_DPI (where DPI denotes the diffraction precision index), has been created to calculate the `Cruickshank DPI' value for a given three-dimensional protein or macromolecular structure. It also estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables users to visualize the computed values dynamically on the client machine. Users can provide the Protein Data Bank (PDB) identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and the atomic coordinate errors for all the atoms are included in the revised PDB file. Further, users can graphically view the atomic coordinate error along with `temperature factors' (i.e. atomic displacement parameters). In addition, the computing engine is interfaced with an up-to-date local copy of the Protein Data Bank. New entries are updated every week, and thus users can access all the structures available in the Protein Data Bank. The computing engine is freely accessible online at http://cluster.physics.iisc.ernet.in/dpi/.
Crystal structure of anagyrine perchlorate
Authors: Turgunov Kambarali K. , Rakhimov Shukhrat B. , Vinogradova Valentina I. , Tashkhodjaev Bakhodir
Published: April 2015

The title molecular salt, C15H21N2O+·ClO4−, crystallizes with four cations (A,B,CandD) and four anions in the chiral unit cell (space groupP21). The alkaloid was isolated from the aerial parts ofGenista Hispanicacollected in the Samarkand region of Uzbekistan. Each cation is protonated at the N atom that bridges the alkaloid ringsCandD. In each cation, ringAis almost planar and ringBadops a sofa conformation with the methylene group bridging to theCring as the flap. RingsCandDadopt chair conformations with acisring junction in all four cations. In the crystal,A+BandC+Ddimeric pairs linked by pairs of N—H...O hydrogen bonds are observed, which generateR22(16) loops in each case. The dimers are consolidated by weak aromatic π–π stacking interactions between theArings [centroid–centroid distances = 3.913 (3) and 3.915 (3) Å].
New insights in the discovery of novelh-MAO-B inhibitors: structural characterization of a series ofN-phenyl-4-oxo-4H-chromene-3-carboxamide derivatives
Authors: Gomes Ligia R. , Low John Nicolson , Cagide Fernando , Chavarria Daniel , Borges Fernanda
Published: April 2015

SixN-substituted-phenyl 4-oxo-4H-chromene-3-carboxamides, namelyN-(2-nitrophenyl)-4-oxo-4H-chromene-3-carboxamide, C16H10N2O5(2b),N-(3-methoxyphenyl)-4-oxo-4H-chromene-3-carboxamide, C17H13NO4, (3a),N-(3-bromophenyl)-4-oxo-4H-chromene-3-carboxamide, C16H10BrNO3, (3b),N-(4-methoxyphenyl)-4-oxo-4H-chromene-3-carboxamide, C17H13NO4, (4a),N-(4-methylphenyl)-4-oxo-4H-chromene-3-carboxamide, C17H13NO3, (4d), andN-(4-hydroxyphenyl)-4-oxo-4H-chromene-3-carboxamide, C16H11NO4, (4e), have been structurally characterized. All compounds exhibit ananticonformation with respect to the C—N rotamer of the amide and atrans-related conformation with the carbonyl groups of the chromone ring of the amide. These structures present an intramolecular hydrogen-bonded network comprising an N—H...O hydrogen bond between the amide N atom and the O atom of the carbonyl group of the pyrone ring, forming anS(6) ring, and a weak Car—H...O hydrogen bond in which the carbonyl group of the amide acts as acceptor for the H atom of anortho-C atom of the exocyclic phenyl ring, which results in anotherS(6) ring. The N—H...O intramolecular hydrogen bond constrains the carboxamide moiety such that it is virtually coplanar with the chromone ring.
Reference group influence in consumer role rehearsal narratives
Authors: Schulz Heather Marie
Published: April 2015

Purpose

– This paper aims to analyse reference group influence through the imagined audience construct of the role theory. Prior research has shown the influential nature of reference groups on an individuals’ behaviour. The studied theatrical metaphor supplies a new perspective to the social phenomenon of reference group dynamics in consumer behaviour.

Design/methodology/approach

– Twenty face-to-face interviews were conducted utilizing a naturalistic research study design. The interviews took place in the participants’ homes, and participants were asked to create five outfits for various social situations. Then, the participants were asked about the outfits they created, and how that outfit aided in their role preparation process. An inductive analysis of the data resulted in narrative themes that align with several role theory constructs.

Findings

– The consumer role rehearsal narratives that emerged describe the process individuals go through for anticipated social interactions. Depending on the social situation, role theory constructs such as role expectations, role location, role learning and role skill were highlighted. The imagined audience of various reference groups do impact the individual’s future behaviours.

Research limitations/implications

– Future researchers could apply additional role theory constructs not only to reference groups but also to other aspects of consumer behaviour as well.

Originality/value

– This paper supplies a role theory framework that can be used by future researchers when studying reference group influence on consumer behaviour.
Why environmentally conscious consumers do not purchase green products
Authors: Barbarossa Camilla , Pastore Alberto
Published: April 2015

Purpose

– This paper aims to address the green purchasing gap by: exploring environmentally conscious consumers’ mental representation of the barriers responsible for the green purchasing gap; assessing which barriers are perceived as the most relevant in hampering the purchase of green products for environmentally conscious consumers; and investigating the relationships among these barriers. Although consumers are increasingly concerned about environmental deterioration, the current market share of green products remains fairly low.

Design/methodology/approach

– An introspective qualitative study is conducted; 51 environmentally conscious consumers showing a green purchasing gap are interviewed, and the data are analysed with a cognitive mapping technique (Decision Explorer software) and Freeman’ structural indices (UCINET software).

Findings

– Higher price and scarce availability of green products are the main barriers to green purchasing. However, consumers’ perceptions of price and availability may vary by changing other barriers (e.g. green products displacement inside the store and in-store communication).

Originality/value

– This work reconstructs the decisional premises of environmentally conscious consumers’ choices to not purchase green products, identifies the most relevant barriers to green purchasing behaviour and the relationships between these barriers. With this knowledge, marketers of green products can focus on the most important barriers so that interventions in these barriers may change environmentally conscious consumers’ perceptions of other related barriers.
Low pathogenicity of anti‐desmoglein 3 immunoglobulin G autoantibodies contributes to the atypical clinical phenotypes in pemphigus
Authors: Saleh Marwah A. , Hashimoto Rena , Kase Yuko , Amagai Masayuki , Yamagami Jun
Published: April 2015

The clinical phenotypes of pemphigus can be explained by the desmoglein (Dsg) compensation theory. However, some atypical cases such as cutaneous pemphigus vulgaris (cPV), in which patients have anti‐Dsg3 antibodies without oral erosions, do not conform to this theory. To explain the discrepancy between clinical phenotypes and anti‐Dsg antibody profiles, the pathogenic strength of immunoglobulin (Ig)G autoantibodies against Dsg3 must be taken into consideration. We analyzed the epitopes and blister‐inducing pathogenic strength of the sera from three patients having IgG against Dsg3 without oral erosions with domain‐swapped recombinant proteins and dissociation assay using cultured normal human epidermal keratinocytes. The results showed that all sera contained IgG directed against the amino terminal EC1 domain of Dsg3, as is found in most PV sera. However, dissociation assays revealed that the pathogenic strength of the anti‐Dsg3 antibodies in all three cases was extremely lower than that of typical PV cases with mucosal involvement. In conclusion, when anti‐Dsg3 IgG antibodies are not sufficient to inhibit the expression of Dsg3 in the oral mucosa, but can inhibit the expression in the skin, skin blisters can result. Therefore, the pathogenicity of anti‐Dsg3 antibodies should be regarded as a key factor contributing to the clinical phenotype in pemphigus patients with conflicting antibody profiles.
Dynamic Olley‐Pakes productivity decomposition with entry and exit
Authors: Melitz Marc J. , Polanec Sašo
Published: April 2015

We propose an extension of the Olley and Pakes () productivity decomposition that accounts for the contributions of surviving, entering, and exiting firms to aggregate productivity changes. We argue that the other decompositions that break down aggregate productivity changes into similar components introduce some biases in the measurement of the contributions of entry and exit. We apply our proposed decomposition to Slovenian manufacturing data and contrast our results with those of other decompositions. We find that, over a five‐year period, the measurement bias associated with entry and exit is substantial, accounting for up to 10 percentage points of aggregate productivity growth.
Gazing at a giraffe gyroscope: where are we going?
Authors: Bercovitch Fred B. , Deacon Francois
Published: April 2015

Giraffe are popular animals to watch while on wildlife safaris, and feature prominently in zoos, advertisements, toys and cartoons. Yet, until recently, few field studies have focused on giraffe. We introduce this giraffe topic issue with a review essay that explores five primary questions: How many (sub) species of giraffe exist? What are the dynamics of giraffe herds? How do giraffe communicate? What is the role of sexual selection in giraffe reproduction? How many giraffe reside in Africa? A confluence of causes has produced drastic declines in giraffe population numbers in Africa, and we conclude that guiding giraffe conservation plans depends upon evaluation of the five key quandaries that we pose.
Are allergic multimorbidities and IgE polysensitization associated with the persistence or re‐occurrence of foetal type 2 signalling? The MeDALL hypothesis
Authors: Bousquet J. , Anto J. M. , Wickman M. , Keil T. , Valenta R. , Haahtela T. , Lodrup Carlsen K. , van Hage M. , Akdis C. , Bachert C. , Akdis M. , Auffray C. , Annesi‐Maesano I. , Bindslev‐Jensen C. , Cambon‐Thomsen A. , Carlsen K. H. , Chatzi L. , Forastiere F. , Garcia‐Aymerich J. , Gehrig U. , Guerra S. , Heinrich J. , Koppelman G. H. , Kowalski M. L. , Lambrecht B. , Lupinek C. , Maier D. , Melén E. , Momas I. , Palkonen S. , Pinart M. , Postma D. , Siroux V. , Smit H. A. , Sunyer J. , Wright J. , Zuberbier T. , Arshad S. H. , Nadif R. , Thijs C. , Andersson N. , Asarnoj A. , Ballardini N. , Ballereau S. , Bedbrook A. , Benet M. , Bergstrom A. , Brunekreef B. , Burte E. , Calderon M. , De Carlo G. , Demoly P. , Eller E. , Fantini M. P. , Hammad H. , Hohman C. , Just J. , Kerkhof M. , Kogevinas M. , Kull I. , Lau S. , Lemonnier N. , Mommers M. , Nawijn M. , Neubauer A. , Oddie S. , Pellet J. , Pin I. , Porta D. , Saes Y. , Skrindo I. , Tischer C. G. , Torrent M. , von Hertzen L.
Published: April 2015

Allergic diseases [asthma, rhinitis and atopic dermatitis (AD)] are complex. They are associated with allergen‐specific IgE and nonallergic mechanisms that may coexist in the same patient. In addition, these diseases tend to cluster and patients present concomitant or consecutive diseases (multimorbidity). IgE sensitization should be considered as a quantitative trait. Important clinical and immunological differences exist between mono‐ and polysensitized subjects. Multimorbidities of allergic diseases share common causal mechanisms that are only partly IgE‐mediated. Persistence of allergic diseases over time is associated with multimorbidity and/or IgE polysensitization. The importance of the family history of allergy may decrease with age. This review puts forward the hypothesis that allergic multimorbidities and IgE polysensitization are associated and related to the persistence or re‐occurrence of foetal type 2 signalling. Asthma, rhinitis and AD are manifestations of a common systemic immune imbalance (mesodermal origin) with specific patterns of remodelling (ectodermal or endodermal origin). This study proposes a new classification of IgE‐mediated allergic diseases that allows the definition of novel phenotypes to (i) better understand genetic and epigenetic mechanisms, (ii) better stratify allergic preschool children for prognosis and (iii) propose novel strategies of treatment and prevention.
Utility of characteristic ‘Weak to Absent’ INI1/SMARCB1/BAF47 expression in diagnosis of synovial sarcomas
Authors: Rekhi Bharat , Vogel Ulrich
Published: April 2015

Recently, very few studies have shown value of immunohistochemical (IHC) expression of INI1/SMARCB1 in diagnosis of synovial sarcomas (SSs). This study was aimed at testing reproducibility and utility of this finding. Sixty‐eight SSs and 147 other tumours, in the form of various biopsies, were tested for IHC expression of INI1. Twenty‐six SSs were further confirmed with positive SS18 rearrangement. Forty monophasic spindle cell type (58.8%), 13 biphasic (19.1%), 12 poorly differentiated (17.6%) and three calcifying SSs (4.4%) were positive for epithelial membrane antigen (EMA) (46/62) (74.1%), pan cytokeratin (AE1/AE3) (31/47) (65.9%), cytokeratin (CK7) (20/31) (64.5%), BCL2 (62/66) (93.9%), MIC2 (61/63) (96.8%), transducin‐like enhancer of split 1 (TLE1) (29/31) (93.5%) and CK19 (14/24) (58.3%). INI1 expression was ‘weak to absent’ in 60/68 (88.2%) SSs; in 1/3 atypical ossifying fibromyxoid tumours (AOFMTs) and in 3/10 (30%) malignant peripheral nerve sheath tumours (MPNSTs) of various types. INI1 was completely absent in 10/10 (100%) epithelioid sarcomas (ESs), 4/4 (100%) malignant rhabdoid tumours, single paediatric undifferentiated sarcoma, 5/19 (26.3%) myoepithelial carcinomas and in 2/4 (50%) epithelioid‐subtype of MPNSTs. Remaining 100 tumours, including 12 Ewing sarcomas, 15 carcinomas, eight solitary fibrous tumours (SFT), seven extraskeletal myxoid chondrosarcomas, three fibrosarcomas and other tumours retained INI1 expression. A unique ‘weak to absent’ IHC expression of INI1 is highly sensitive (88.2%) and specific (97.3%) for a SS, irrespective of its subtypes and types of biopsies. This can be considered useful in diagnosing SSs, especially in settings lacking molecular and/or cytogenetic analysis. A similar INI1 expression is shared by certain AOFMTs and MPNSTs.
No relevant pharmacokinetic interaction between pantoprazole and mycophenolate in renal transplant patients: a randomized crossover study
Authors: Rissling Olesja , Glander Petra , Hambach Pia , Mai Marco , Brakemeier Susanne , Klonower Daniela , Halleck Fabian , Singer Eugenia , Schrezenmeier Eva‐Vanessa , Dürr Michael , Neumayer Hans‐Hellmut , Budde Klemens
Published: April 2015

Aims

Mycophenolic acid (MPA) suppresses lymphocyte proliferation through inosine monophosphate dehydrogenase (IMPDH) inhibition. Two formulations have been approved: mycophenolate mofetil (MMF) and enteric‐coated mycophenolate sodium (EC‐MPS). Pantoprazole (PAN) inhibits gastric acid secretion, which may alter MPA exposure. Data from healthy volunteers suggest a significant drug–drug interaction (DDA) between pantoprazole and MPA. In transplant patients, a decreased MPA area under the concentration–time curve (AUC) may lead to higher IMPDH activity, which may lead to higher acute rejection risk. Therefore this DDA was evaluated in renal transplant patients under maintenance immunosuppressive therapy.

Methods

In this single‐centre, open, randomized, four‐sequence, four‐treatment crossover study, the influence of PAN 40 mg on MPA pharmacokinetics such as (dose‐adjusted) AUC0–12 h (dAUC) was analysed in 20 renal transplant patients (>6 months post‐transplantation) receiving MMF (1–2 g day–1) and EC‐MPS in combination with ciclosporin. The major metabolite MPA glucuronide (MPAG) and the IMPDH activity were also examined.

Results

MMF + PAN intake led to a lowest mean dAUC for MPA of 41.46 ng h ml–1 mg–1 [95% confidence interval (CI) 32.38, 50.54], while MPA exposure was highest for EC‐MPS + PAN [dAUC: 46.30 ng h ml–1 mg–1 (95% CI 37.11, 55.49)]. Differences in dAUC and dose‐adjusted maximum concentration (dCmax) were not significant. Only for MMF [dAUC: 41.46 ng h ml–1 mg–1 (95% CI 32.38, 50.54)] and EC‐MPS [dAUC: 43.39 ng h ml–1 mg–1 (95% CI 33.44, 53.34)] bioequivalence was established for dAUC [geometric mean ratio: 101.25% (90% CI 84.60, 121.17)]. Simultaneous EC‐MPS + PAN intake led to an earlier time to Cmax (tmax) [median: 2.0 h (min–max: 0.5–10.0)] than EC‐MPS intake alone [3 h (1.5–12.0); P = 0.037]. Tmax was not affected for MMF [1.0 h (0.5–5.0)] ± pantoprazole [1.0 h (0.5–6.0), P = 0.928). No impact on MPAG pharmacokinetics or IMPDH activity was found.

Conclusion

Pantoprazole influences EC‐MPS and MMF pharmacokinetics but as it had no impact on MPA pharmacodynamics, the immunosuppressive effect of the drug was not impaired.