bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of archived chemical shifts through atomic coordinates
Authors: Rieping Wolfgang , Vranken Wim F. 
Published: April 2010

AbstractThe public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per‐atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per‐entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries (http://www.ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift‐based methods in NMR. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Key issues with implementing LOPA
Authors: Bridges William Bill , Clark Tony 
Published: April 2010

AbstractThis article writen by one of the originators of LOPA, focuses on problems observed with LOPA.
One the biggest issues is that organizations use LOPA without following the rules for LOPA, especially the rules related to maintaining, testing, and record‐keeping for each independent protection layer (IPL) and for each “optimized” initiating event (IE).
Another issue is that many companies and analysts overuse LOPA. The LOPA book authors expected the number of scenarios going to LOPA (after a HAZOP/PHA) would be 1 to 10% (max) of those uncovered in a qualitative analysis (maybe after 100 HAZOP nodes, you would do 1–10 LOPA). A PHA team would recommend (or use) LOPA only if the scenario was too complex for the PHA/HAZOP team. It appears that most companies are using LOPA for every scenario that has a severe consequence; this result in doing LOPA on much more than 10% of the scenarios.
Many times, there is weak definition of the consequence that is being avoided, so an independent layer of protection does not always match up well with the consequence.
LOPA is also overworked when it is used. Many of us on the original LOPA book authorship considered LOPA a single analyst job, after a PHA/HAZOP. Instead, the trend appears to be that companies (or perhaps their consultants) make LOPA part of the PHA (in situ), therefore involving the whole PHA team.
LOPA is used in PHA team settings, which distracts PHA teams from their primary task of brainstorming to identify the accident scenarios that can occur.
This article focuses on preventing these problems and also summarizes the many benefits LOPA has produced for the industry. © 2010 American Institute of Chemical Engineers Process Saf Prog, 2010
Bayesian data analysis
Authors: Kruschke John K. 
Published: April 2010

AbstractBayesian methods have garnered huge interest in cognitive science as an approach to models of cognition and perception. On the other hand, Bayesian methods for data analysis have not yet made much headway in cognitive science against the institutionalized inertia of 20th century null hypothesis significance testing (NHST). Ironically, specific Bayesian models of cognition and perception may not long endure the ravages of empirical verification, but generic Bayesian methods for data analysis will eventually dominate. It is time that Bayesian data analysis became the norm for empirical methods in cognitive science. This article reviews a fatal flaw of NHST and introduces the reader to some benefits of Bayesian data analysis. The article presents illustrative examples of multiple comparisons in Bayesian analysis of variance and Bayesian approaches to statistical power. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:Psychology > Theory and Methods
Imitation: what animal imitation tells us about animal cognition
Authors: Bates Lucy A. , Byrne Richard W. 
Published: April 2010

AbstractImitation of actions is widespread in the animal kingdom, but the mental capacities thereby implied vary greatly according to the adaptive function of copying. Behavioral synchrony in social species has many possible benefits, including minimizing predation risk and using food resources optimally, but can be understood by the simple cognitive mechanism of response facilitation by priming. Imitation can send a social message, either one of short‐term meshing or group identity. Where the imitative match is opaque, as in neonatal imitation, the correspondence problem may imply an innate system of behavior matching; but in other cases, no more than priming may be involved, although there are persistent suggestions that great ape imitation implies empathic abilities. Imitation in the service of learning new skills by following another's example can be divided into contextual imitation (when to employ a familiar action, and to what problem) and production imitation (learning of new skills by imitation). Cognitively, the former requires little more than response facilitation, whereas production imitation needs at least the ability to extract the statistical regularities of repeated action and to incorporate the result into hierarchical program construction. Among our close relatives, only the great apes show much evidence of production imitation of actions, along with the ability to selectively imitate the most rational components of what they observe. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:Psychology > Comparative Psychology
Phenomenological elastoplasticity view on strain recovery loops characterizing shape memory material
Authors: Xiao H. , Bruhns O.T. , Meyers A. 
Published: April 2010

AbstractFinite elastoplastic J2‐flow models with combined hardening are found to exhibit strain recovery effects. For uniaxial deformation of bars, these models produce plastic flow with the axial stress growing beyond the initial yield stress and then generate reverse plastic flow with the axial stress reducing to zero. A novel method in terms of parametric variable representations via the plastic work is proposed to study such two‐way plastic flow. By means of this new method, it is shown that the foregoing two‐way plastic flow may give rise to any given shape of strain recovery loops, and, furthermore, explicit models are constructed with strain recovery loops formed by two‐way plastic flow. In conjunction with the parametric variable representation method proposed, these findings suggest the possibility of applying straightforward, classical elastoplasticity models to characterizing pseudoelastic behaviour of shape memory materials.
Through the service operations strategy looking glass: Influence of industrial sector, ownership, and service offerings on B2B e‐marketplace failures
Authors: Rosenzweig Eve D. , Laseter Timothy M. , Roth Aleda V. 
Published: April 2010

AbstractThis paper contributes to the emerging area of e‐service strategy in the context of business‐to‐business (B2B) e‐marketplaces, which we view as Internet‐based service delivery systems that link sellers’ offerings to buyers. Although a myriad of new B2B e‐marketplaces were launched over the past decade, a substantial number failed shortly after the peak of the NASDAQ in 2000. The bursting of the Internet bubble provides a setting for assessing salient, theory‐based determinants of failure—and success. Accordingly, we apply a service operations strategy lens and complementary organizational theories to explain how three strategic factors—industrial sector characteristics, ownership structure, and functionality of service offering—may have influenced B2B e‐marketplaces’ odds of survival after the bubble. We empirically test these factors using logistic regression analysis on a sample of 854 B2B e‐marketplaces.Consistent with emerging e‐services literature, our empirical results indicate that B2B e‐marketplaces serving industrial sectors that are a better fit with the Internet service delivery systems—by high information dependence and low information tacitness—have the highest likelihood of success, as do e‐marketplaces with service offerings that facilitate collaboration among multiple buyers and sellers. We also demonstrate the positive influence of consortium ownership structure on B2B e‐marketplace survival, albeit not for first‐mover consortia‐backed e‐marketplaces. Our findings contribute to the service operations strategy literature and provide direction for managers in the areas of e‐service strategy and investment.
Lithospheric structure and Mesozoic geodynamics of the eastern Central Asian orogen
Authors: Didenko A.N. , Kaplun V.B. , Malyshev Yu.F. , Shevchenko B.F. 
Published: April 2010

AbstractThe lithospheric structure of several marginal and interior units of the eastern Central Asian orogen has been explored in 2D geophysical models. The obtained constraints on effective parameters (density, resistivity, temperature) of lithospheric blocks and their boundaries allowed correlation of geophysical structures to tectonic settings. The geological and geophysical (including paleomagnetic) data were used jointly to model the present structure of the lithosphere along 126° E between 56° N and 40° N and to construct a palinspastic model of the same area for the latest Early Jurassic (175 Ma).
Biogenic sedimentation factors of mineralization in the Neoproterozoic strata of the Baikal–Patom region
Authors: Nemerov V.K. , Stanevich A.M. , Razvozzhaeva E.A. , Budyak A.E. , Kornilova T.A. 
Published: April 2010

Abstract
The formation environments of stratiform ore deposits in the Neoproterozoic Baikal–Patom region (BPR) have been considered. A model for the formation of the Sukhoi Log gold ore deposit in the Bodaibo zone has been put forward. The first stage is gold concentration by a chemolithotrophic bacterial community. Independently established facts suggest that bacterial communities may also have contributed to initial metal accumulation in the sediments of the Kholodnaya Pb–Zn deposit. The ore beds occur in the high-carbon sediments of the side and trough of a back-arc basin. Sedimentation (Dal’nyaya Taiga and Zhuya regional horizons) took place during the “back-arc basin–foreland basin” transition. This transition is characterized by increased sediment bioproductivity, which is clearly evidenced from the increased biophile-element content and taxonomic diversity of organic remains. Hundreds of microfossil sites in the Neoproterozoic BPR host littoral benthos (cyanobacteria and brown algae) and plankton (green algae). Most microfossils in the outer shelf, on the basin side, and in its trough belong to chemolithotrophic bacteria. These bacteria are assumed to have accumulated metals in the vent field of the back-arc basin. Studies showed the ability of microorganisms (bacteria, algae, fungi, etc.) to accumulate Fe, Mn, Au, Pb, Zn, and other metals. Bacterial communities are particularly important for metal accumulation in the vent fields of rift zones and areas of arc volcanism. All these conditions were observed in the Neoproterozoic BPR.
High-density lipoprotein subclasses are a potential intermediary between alcohol intake and reduced risk of cardiovascular disease: The Rancho Bernardo Study
Authors: Muth Natalie D. , Laughlin Gail A. , von Mühlen Denise , Smith Sidney C. , Barrett-Connor Elizabeth 
Published: April 2010

We conducted a cross-sectional study of NMR-derived HDL subclasses and alcohol intake among 2171 community-dwelling older adults with a large proportion of daily or near-daily alcohol consumers (44 %). We aimed to assess whether, in addition to increasing total HDL, alcohol may induce a beneficial shift in HDL particle size distribution. Participants were categorised based on reported alcohol intake (g per week) and on frequency (none, < 3 times/week, 3–4 times/week, ≥ 5 times/week). The association between alcohol intake and lipoprotein fractions was examined using sex-specific linear regression models adjusted for age, BMI, diabetes, current smoking, exercise and hormone therapy in women. There was a stepwise gradient with the highest weekly alcohol consumption associated with the highest total HDL size and greatest number of medium and large HDL particles, as well as higher total HDL concentrations (allP < 0·001); total small HDL did not differ. Alcohol–HDL size associations were similar in both sexes and did not differ by use of hormone replacement therapy in women. In conclusion, regular alcohol consumers had a higher number and percentage of large HDL particles than non-drinkers. These results suggest that one way that alcohol may decrease CVD is through potentially favourable changes in lipoprotein subclass composition.
Paediatric aerodigestive foreign bodies: remember the nasopharynx
Authors: MacNeil S D , Moxham J P , Kozak F K 
Published: April 2010

AbstractIntroduction:Nasopharyngeal foreign bodies are relatively uncommon, compared with other aerodigestive sites. They may mimic a lower airway location, or may be coughed up into the nasopharynx prior to endoscopic evaluation.Objective:To describe our experience with nasopharyngeal foreign bodies mimicking a more distal airway location.Method:Case series from a tertiary referral children's hospital.Results:We present a series of four children who were initially thought to have a lower aerodigestive tract foreign body (three respiratory, one oesophageal), but who were finally diagnosed with nasopharyngeal foreign body. The concept of panendoscopy at all foreign body removals is suggested as a means to avoid a missed nasopharyngeal foreign body.Conclusion:Although nasopharyngeal foreign bodies are uncommon, their rare ability to mimic distal sites mandates a thorough endoscopic approach to ensure that all sites (i.e. larynx, lungs, oesophagus and nasopharynx) are evaluated endoscopically.
Evaluation of computed tomography virtual bronchoscopy in paediatric tracheobronchial foreign body aspiration
Authors: Bhat K V , Hegde J S , Nagalotimath U S , Patil G C 
Published: April 2010

AbstractObjective:Virtual bronchoscopy is a noninvasive technique which provides an intraluminal view of the tracheobronchial tree. This study aimed to evaluate this technique in comparison with rigid bronchoscopy, in paediatric patients with tracheobronchial foreign bodies undetected by plain chest radiography.Methods:Plain chest radiography was initially performed in 40 children with suspected foreign body aspiration. Computed tomography virtual bronchoscopy was performed in the 20 in whom chest radiography appeared normal. Virtual bronchoscopic images were obtained. All patients underwent rigid bronchoscopy performed by an otolaryngologist blinded to the computed tomography virtual bronchoscopy findings, within 24 hours. Virtual bronchoscopic findings were then compared with the results of rigid bronchoscopy.Results:In 12 patients, foreign bodies detected by virtual bronchoscopy were confirmed by rigid bronchoscopy. In one case, a mucous plug was perceived as a foreign body on virtual bronchoscopy. In another case, a minute foreign body was missed on virtual bronchoscopy. The following parameters were calculated: sensitivity, 92.3 per cent; specificity, 85.7 per cent; validity, 90 per cent; positive likelihood ratio, 6.45; and negative likelihood ratio, 0.089.Conclusion:In the presence of a positive clinical diagnosis and negative chest radiography, computed tomography virtual bronchoscopy must be considered in all cases of tracheobronchial foreign body aspiration, in order to avoid needless rigid bronchoscopy. Computed tomography virtual bronchoscopy is particularly useful in screening cases of occult foreign body aspiration, as it has high sensitivity, specificity and validity.
Radiological airway changes following bipolar radiofrequency volumetric tissue reduction
Authors: Heywood R L , Khalil H M B , Kothari S , Chawda S , Kotecha B T 
Published: April 2010

AbstractObjective:To characterise the appearance of lesions of the tongue base and soft palate induced by bipolar radiofrequency volumetric tissue reduction, using magnetic resonance imaging up to six weeks post-procedure.Methods:Five men with sleep-disordered breathing were treated with one session of bipolar radiofrequency volumetric tissue reduction to a number of sites, including the tongue base and soft palate. Magnetic resonance imaging was performed pre-operatively and one week and six weeks after surgery.Results:Lesions were visible from day one. T1 (spine lattice relaxation Time)-weighted images demonstrated areas of central hyperintensity, reflecting haemorrhagic, coagulative necrosis, surrounded by hypointensity, representing oedema; corresponding short tau inversion recovery (STIR) sequences showed central hypointensity with surrounding high signal. The lesions expanded up to day three and then gradually diminished, but were still evident at week six on short tau inversion recovery images.Conclusion:The characterisation of lesions induced by bipolar radiofrequency volumetric tissue reduction enables us to elucidate the pathophysiology of this procedure, to optimise treatment benefits and clinical outcomes, and to explain patient symptoms.
Changing sink demand of developing shoot affects transitory starch biosynthesis in embryonic tissues of germinating rice seeds
Authors: Liu Shiang-Lin , Siao Wei , Wang Shu-Jen 
Published: April 2010

AbstractThe mechanism of starch metabolism in the endosperm of germinating rice (Oryza sativaL.) seed (caryopsis) has been well studied; however, little is known about the occurrence and function of transitory starch in germinating rice embryos. During rice seed germination and seedling establishment, starch in the endosperm is hydrolysed to glucose, which is taken up by scutellar epithelial cells, converted to sucrose, and transported through vascular bundles to other embryonic tissues, such as growing shoots and roots. In this study, we found that soluble sugar was converted to starch in the scutellum 6 d after imbibition (DAI). Starch appeared primarily in cells surrounding the vascular bundles of the embryonic axis 12 DAI. The removal of growing shoots caused hyper-accumulation of starch in embryonic tissues, including the scutellum. In contrast, placing seedlings in the dark, which reduced photosynthetic efficiency, lowered starch levels in the embryonic axis cells. The disappearance of transitory starch from embryonic tissues of dark-grown seedlings was accompanied by a reduction of soluble sugar content and the down-regulation of the expression and activity of starch biosynthesis enzymes. These results suggest that the amount of transitory starch in embryonic tissues was dependent on the demand of growing sink tissues.
Mouse sarcoma L1 cell line holoclones have a stemness signature
Authors: Miloszewska J. , Gos M. , Przybyszewska M. , Trembacz H. , Koronkiewicz M. , Janik P. 
Published: April 2010

AbstractAccumulating data suggest that cancers contain a fraction of cells called cancer stem cells (CSCs), that may be responsible for upkeep and relapses of disease. In experimental settings, CSCs are regarded as most effective at tumour initiation in in vivo assays. Since the first isolation of cancer stem cells from acute myeloid leukaemia in 1994, cancer stem cells have been identified in human solid tumours and they have also been found in the established cell lines, based on ability of CSCs to form in vitro colonies of a specific morphology, called holoclones. Our study examined the ability of a mouse sarcoma cell line, derived from a lung metastasis of a BALB/c mouse and established as a stably growing line (L1), to produce holoclones in vitro. We aimed to verify a stemness signature of the holoclone cells. The L1 cell line was found to form holoclone colonies in vitro, which were shown to contain a percentage of CSC‐like cells. A fraction of the L1 cells was able to repopulate the original cell line, and presented an increased clonogenic and metastatic potential (18th passage). In addition, MTT assay and flow cytometry of the side population fraction revealed that these cells were more resistant to chemotherapeutic drugs than the original cell line, and over‐expressed the anti‐apoptotic genes, GRP78 and GADD153. We conclude that mouse L1 sarcoma cell line contains CSC‐like cells.
Epidermal kinetic alterations required to generate the psoriatic phenotype: a reappraisal
Authors: Simonart T. , Heenen M. , Lejeune O. 
Published: April 2010

AbstractObjectives:  Although there have been major advances in understanding immunopathogenesis of psoriasis, the basic processes causing psoriatic morphology remain to be identified.Materials and methods:  Our group has designed a systematic review of studies (1962–2009) on keratinocyte kinetics in psoriasis. We obtained data from MEDLINE, PubMed, Current Contents, reference lists and specialist textbooks. A general equation for evolution of the differentiated epidermis has been analysed. Necessary conditions for observed qualitative change in homeostasis between normal skin and established psoriatic lesions were determined.Results and discussion:  Increase in the number of cell divisions (or imbalance in symmetric division rates of committed progenitor cells) and/or decrease in physiological apoptosis in the germinative compartment, together with feedback loops that limit thickening of the skin, are required to generate psoriatic morphology, that is, to increase the absolute size but decrease relative size of the differentiated cell compartment with respect to the germinative compartment.
What's in a service?
Authors: Axford Nick 
Published: April 2010

ABSTRACTThe measurement of ‘service’ in children's services is highly varied. We do not know in a meaningful sense what services children and families get. This paper sets out why it is important to measure services well. It outlines the dimensions of ‘service’, how they have been measured in research, policy and practice contexts, and the strengths and weaknesses of these approaches. It then explores implications for the field and identifies potential applications of a more nuanced and consistent approach to measuring services.