bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multilayer evaluation approach for protein structure prediction and model quality assessment
Authors: Zhang Jingfen , Wang Qingguo , Vantasin Kittinun , Zhang Jiong , He Zhiquan , Kosztin Ioan , Shang Yi , Xu Dong 
Published: September 2011

AbstractProtein tertiary structures are essential for studying functions of proteins at molecular level. An indispensable approach for protein structure solution is computational prediction. Most protein structure prediction methods generate candidate models first and select the best candidates by model quality assessment (QA). In many cases, good models can be produced, but the QA tools fail to select the best ones from the candidate model pool. Because of incomplete understanding of protein folding, each QA method only reflects partial facets of a structure model and thus has limited discerning power with no one consistently outperforming others. In this article, we developed a set of new QA methods, including two QA methods for evaluating target/template alignments, a molecular dynamics (MD)‐based QA method, and three consensus QA methods with selected references to reveal new facets of protein structures complementary to the existing methods. Moreover, the underlying relationship among different QA methods were analyzed and then integrated into a multilayer evaluation approach to guide the model generation and model selection in prediction. All methods are integrated and implemented into an innovative and improved prediction system hereafter referred to as MUFOLD. In CASP8 and CASP9, MUFOLD has demonstrated the proof of the principles in terms of both QA discerning power and structure prediction accuracy. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Analysis of independent protection layers used in three typical chemical processes
Authors: Meyer Herbert W.H. 
Published: September 2011

AbstractIndependent protection layers (IPLs) used to mitigate the most severe consequences are analyzed for three chemical processes. The IPLs are categorized by type, function, and design. An analysis of management systems that are in place to ensure the integrity of the IPLs is also included. Categorizations for all three plants revealed similar results and suggest that the results extend across the chemical industry. The data show that the chemical plants depend much more heavily on IPLs that prevent an incident rather than respond to an incident once hazardous material is released. The survey also found that there is a significant reliance on administrative safeguards to achieve an acceptable level of risk. Recommendations are made on how administrative safeguards can adapt these systems to improve their robustness. © 2011 American Institute of Chemical Engineers Process Saf Prog, 2011
Testing interruptions in reactive systems
Authors: Andrade Wilkerson L. , Machado Patrícia D. L. 
Published: September 2011

Abstract
Modelling and testing of reactive systems with interruptions are discussed. These systems are commonly found in portable devices, where interruptions to a running application can be demanded at any time, due to concurrent execution of processes sharing a single resource, such as screen, as well as arrival of calls from network distributed services. Since the possible number of combinations of allowed interruptions is large, proper test case selection activities need to be performed. But, in order to systematically investigate and select test cases, it is fundamental to explicitly model interruption behaviour in a compositional way, avoiding the need for explicit enumeration. This work presents a strategy for testing interruptions in reactive systems that covers modelling for testing of systems with interruptions, generation and selection of sound test cases. The strategy is supported by the LTS-BT tool. Moreover, a formal model of an environment devoted to execution of test cases with interruptions is presented. Finally, a case study illustrates its applicability in the mobile phone application domain.
Bioavailability of vitamin C from mashed potatoes and potato chips after oral administration in healthy Japanese men
Authors: Kondo Yoshitaka , Higashi Chihana , Iwama Mizuki , Ishihara Katsuyuki , Handa Setsuko , Mugita Hiroyuki , Maruyama Naoki , Koga Hidenori , Ishigami Akihito 
Published: September 2011

Potato (Solanum tuberosum) tubers contain vitamin C (VC) and commercial potato chips have more VC content per wet weight by dehydration during frying. However, intestinal absorption of VC from orally ingested potatoes and its transfer to the blood remains questionable. The present study was designed to determine whether the dietary consumption of potatoes affects VC concentration in plasma and urinary excretion of VC in human subjects. After overnight fasting, five healthy Japanese men between 22 and 27 years of age consumed 87 g mashed potatoes and 282 g potato chips. Each portion contained 50 mg of VC, 50 mg VC in mineral water and mineral water. Before and after a single episode of ingestion, blood and urine samples were collected every 30 min or 1 h for 8 h. When measured by subtraction of the initial baseline value before administration of potatoes from the values measured throughout the 8 h test period, plasma VC concentrations increased almost linearly up to 3 h. Subsequently, the values of potato-fed subjects were higher than those of water, but did not differ significantly from those of VC in water (P = 0·14 andP = 0·5). Less VC tended to be excreted in urine during the 8 h test than VC in water alone (17·0 (sem7·5) and 25·9 (sem8·8)v.47·9 (sem17·9) μmol/mmol creatinine). Upon human consumption, mashed potatoes and potato chips provide VC content that is effectively absorbed in the intestine and transferred to the blood. Clearly, potatoes are a readily available source of dietary VC.
Policy Dynamism: The Case of Aboriginal Australian Education
Authors: MOORE TERRY 
Published: September 2011

AbstractWith reference to an ethnographic study of Aboriginal Australians in formal schooling, this paper focuses on the dynamism of the policy process. It argues that social policy is different in its performance from its formal articulation. It proposes that other discourses complicate policy discourse in its implementation, and that the Aboriginal objects of policy respond creatively to their representation in policy in ways that contribute to that complication. Aboriginal political leaders adopt the subject imagined in policy, elaborate its normativity and pressure their constituency to perform it. The routine performance of this subject works to compromise individuals’ capabilities to negotiate their lived interculturality and multiplicity, and confirms Aborigines in their marginalisation. Thus, policy becomes a central, authoritative catalyst in the real-world constitution of the subject initially imagined. The paper proposes that if social policy engages with this complexity, it can be effective in its aims of contributing to Aboriginal education and development, and management of the emerging condition of diversity. In both cases, it must account for the discursive and performative agency of the objects of policy, making it necessarily context-specific and revisable.
Three-dimensional path planning for unmanned aerial vehicle based on linear programming
Authors: Chen Yang , Han Jianda , Zhao Xingang 
Published: September 2011

SUMMARYIn this paper, an approach based on linear programming (LP) is proposed for path planning in three-dimensional space, in which an aerial vehicle is requested to pursue a target while avoiding static or dynamic obstacles. This problem is very meaningful for many aerial robots, such as unmanned aerial vehicles. First, the tasks of target-pursuit and obstacle-avoidance are modelled with linear constraints in relative coordination according to LP formulation. Then, two weighted cost functions, representing the optimal velocity resolution, are integrated into the final objective function. This resolution, defined to achieve the optimal velocity, deals with the optimization of a pair of orthogonal vectors. Some constraints, such as boundaries of the vehicle velocity, acceleration, sensor range, and flying height, are considered in this method. A number of simulations, under static and dynamic environments, are carried out to validate the performance of generating optimal trajectory in real time. Compared with ant colony optimization algorithm and genetic algorithm, our method has less parameters to tune and can achieve better performance in real-time application.
Quorum quenching quandary: resistance to antivirulence compounds
Authors: Maeda Toshinari , García-Contreras Rodolfo , Pu Mingming , Sheng Lili , Garcia Luis Rene , Tomás Maria , Wood Thomas K 
Published: September 2011

Abstract
Quorum sensing (QS) is the regulation of gene expression in response to the concentration of small signal molecules, and its inactivation has been suggested to have great potential to attenuate microbial virulence. It is assumed that unlike antimicrobials, inhibition of QS should cause less Darwinian selection pressure for bacterial resistance. Using the opportunistic pathogen Pseudomonas aeruginosa, we demonstrate here that bacterial resistance arises rapidly to the best-characterized compound that inhibits QS (brominated furanone C-30) due to mutations that increase the efflux of C-30. Critically, the C-30-resistant mutant mexR was more pathogenic to Caenorhabditis elegans in the presence of C-30, and the same mutation arises in bacteria responsible for chronic cystic fibrosis infections. Therefore, bacteria may evolve resistance to many new pharmaceuticals thought impervious to resistance.
Accessing protein conformational ensembles using room-temperature X-ray crystallography
Authors: Fraser James S. , van den Bedem Henry , Samelson Avi J. , Lang P. Therese , Holton James M. , Echols Nathaniel , Alber Tom 
Published: September 2011

Modern protein crystal structures are based nearly exclusively on X-ray data collected at cryogenic temperatures (generally 100 K). The cooling process is thought to introduce little bias in the functional interpretation of structural results, because cryogenic temperatures minimally perturb the overall protein backbone fold. In contrast, here we show that flash cooling biases previously hidden structural ensembles in protein crystals. By analyzing available data for 30 different proteins using new computational tools for electron-density sampling, model refinement, and molecular packing analysis, we found that crystal cryocooling remodels the conformational distributions of more than 35% of side chains and eliminates packing defects necessary for functional motions. In the signaling switch protein, H-Ras, an allosteric network consistent with fluctuations detected in solution by NMR was uncovered in the room-temperature, but not the cryogenic, electron-density maps. These results expose a bias in structural databases toward smaller, overpacked, and unrealistically unique models. Monitoring room-temperature conformational ensembles by X-ray crystallography can reveal motions crucial for catalysis, ligand binding, and allosteric regulation.
A revised target strength–length estimate for blue whiting (Micromesistius poutassou): implications for biomass estimates
Authors: Pedersen Geir , Godø Olav Rune , Ona Egil , Macaulay Gavin J. 
Published: September 2011

Abstract
Pedersen, G., Godø, O. R., Ona, E., and Macaulay, G. J. 2011. A revised target strength–length estimate for blue whiting (Micromesistius poutassou): implications for biomass estimates. – ICES Journal of Marine Science, 68: 2222–2228. Acoustic abundance estimates of blue whiting have generally been higher than estimates based on catch data. One explanation has been that the relationship between acoustic target strength (TS) and length is too low and hence overestimates the number of fish. Measurements of TS were conducted during surveys of blue whiting in March/April 2003–2007 to the west of the British Isles from several different measurement platforms, and also during August 2005 in the Norwegian Sea. Results from these experiments confirm the view that the existing TS–length relationship is too low. A new TS–length relationship is proposed that is ∼5 dB higher. Blue whiting TS is considerably higher than observed and modelled for a similar species, southern blue whiting (Micromesistius australis).
Behaviour of Atlantic cod, a marine fish predator, during Atlantic salmon post-smolt migration
Authors: Hedger Richard D. , Uglem Ingebrigt , Thorstad Eva B. , Finstad Bengt , Chittenden Cedar M. , Arechavala-Lopez Pablo , Jensen Arne J. , Nilsen Rune , Økland Finn 
Published: September 2011

AbstractHedger, R. D., Uglem, I., Thorstad, E. B., Finstad, B., Chittenden, C. M., Arechavala-Lopez, P., Jensen, A. J., Nilsen, R., and Økland, F. 2011. Behaviour of Atlantic cod, a marine fish predator, during Atlantic salmon post-smolt migration. – ICES Journal of Marine Science, 68: 2152–2162. Acoustic telemetry was used to determine the behavioural strategies of Atlantic cod (Gadus morhua) during Atlantic salmon (Salmo salar) post-smolt migration within a Norwegian fjord (Eresfjord). In all, 38 adult cod captured in the inner fjord were tagged with acoustic transmitters in 2008 and 2009, and their behaviour was determined using a fixed hydrophone array. Cod tended to aggregate in the innermost part of the fjord, occupying distinct demersal home territories, showing horizontal movements consistent with foraging. Tidal influences were not observed; cod spent more time near the surface at night. Cod behaviour during peak post-smolt migration differed from that before and after migration. First, cod tended to have more-focused spatial distributions during peak post-smolt migration, consistent with them not having to forage so far when prey were available in abundance. Second, some half the cod were detected nocturnally (but rarely during daylight) near the river mouth during peak post-smolt migration, consistent with them feeding on nocturnally migrating post-smolts. Third, cod were more common near the surface, consistent with them feeding on post-smolts migrating through near-surface waters. These patterns, however, were not shown by all the cod, suggesting that this opportunistic feeder was also preying on other species.
Cushing’s syndrome in multiple endocrine neoplasia type 1
Authors: Simonds William F. , Varghese Sarah , Marx Stephen J. , Nieman Lynnette K. 
Published: September 2011

SummaryObjective  In patients with multiple endocrine neoplasia type 1 (MEN1), Cushing’s syndrome (CS) from endogenous hypercortisolism can result from pituitary, adrenal or other endocrine tumours. The purpose of this study was to characterize the range of presentations of CS in a large series of MEN1 patients.Design  Retrospective review of NIH Clinical Center inpatient records over an approximately 40‐year period.Patients  Nineteen patients (eight males, 11 females) with CS and MEN1.Measurements  Biochemical, imaging, surgical and pathological findings.Results  An aetiology was determined for 14 of the 19 patients with CS and MEN1: 11 (79%) had Cushing’s disease (CD) and three (21%) had ACTH‐independent CS owing to adrenal tumours, frequencies indistinguishable from sporadic CS. Three of 11 MEN1 patients with CD (27%) had additional non‐ACTH‐secreting pituitary microadenomas identified at surgery, an incidence 10‐fold higher than in sporadic CD. Ninety‐one per cent of MEN1 patients with CD were cured after surgery. Two of three MEN1 patients with ACTH‐independent CS (67%) had adrenocortical carcinoma. One patient with adrenal cancer and another with adrenal adenoma were cured by unilateral adrenalectomy. No case of ectopic ACTH secretion was identified in our patient cohort. The aetiology of CS could not be defined in five patients; in three of these, hypercortisolism appeared to resolve spontaneously.Conclusions  The tumour multiplicity of MEN1 can be reflected in the anterior pituitary, MEN1‐associated ACTH‐independent CS may be associated with aggressive adrenocortical disease and an aetiology for CS in MEN1 may be elusive in a substantial minority of patients.
Socioeconomic status and children with intellectual disability in China
Authors: Zheng X. , Chen R. , Li N. , Du W. , Pei L. , Zhang J. , Ji Y. , Song X. , Tan L. , Yang R. 
Published: September 2011

AbstractBackground  Intellectual disability (ID) accounts for 70% of all disabilities among children in China's Second National Sampling Survey on Disability. Although studies have shown a relationship between social class and ID in children, none have investigated the association of socioeconomic variables in Chinese children with mild or severe ID.Methods  Data for children aged 0–6 years with and without ID were abstracted from the Second National Sampling Survey on Disability in China, conducted in 2006. Crude odds ratios showed the effect of sociodemographic factors on mild and severe ID. Adjusted odds ratios (ORa) (95% confidence intervals) estimated the independent effects of these factors.Results  For both mild and severe ID, risk of having ID increased with male sex, birth to a woman aged 35 years and older, lower maternal education, mother's older age at delivery, lower income and rural residence. After age, gender and parent disability were controlled, mothers aged 35 years and older were more likely to have a child with ID: mild ID, ORa 1.47 (1.15–1.88); severe ID, ORa 1.32 (1.00–1.73). There was an approximate increasing monotonic risk of severe ID with increasing socioeconomic disadvantage: lowest income, ORa 3.00 (2.19–4.12); low income, ORa 2.28 (1.63–3.19); lower middle income, ORa 1.72 (1.27–2.33); middle income, ORa 1.73 (1.28–2.36).Conclusions  There is a significant relationship between sociodemographic factors and ID. Similar patterns were found for both mild and severe ID. Recommendations are given for preventing ID in Chinese children.
Models of care delivery in mental health nursing practice: a mixed method study
Authors: CARLYLE D. , CROWE M. , DEERING D. 
Published: September 2011

Accessible summary
Mental health nursing care is usually delivered in multidisciplinary teams within inpatient and outpatient settings. This team approach to care delivery is underpinned by an assumption of a common set of values and a common model of care delivery among disciplines.
Mental health nurses appear to endorse a range of explanatory conceptual models as important in respect to aetiology, treatment, and factors influencing improvement, the role of the mental health service and the role of nurses. This study found that although the participants used a psychodynamic framework for understanding the causes of mental distress they described the presenting problems and the nursing interventions in terms of supporting a medical model of care.
Mental health nursing care is subjugated by a medical model which constrains the possibilities for mental health nursing interventions. This then potentially creates tension between what nurses believe to be the problem and the responses available for nurses in their clinical setting.
AbstractThe aim of this study was to identify the conceptual models that underpin mental health nursing care in clinical settings. This study is a modification of a previous study which evaluated the influence of implicit models of mental disorder on processes of decision making within community‐based teams. Participants completed questionnaires in response to a scenario. A range of explanatory conceptual models were identified in respect to aetiology, treatment and recovery. In a forced choice the participants ranked a medical model of care above other models as underpinning care delivery. The content analysis found that the participants used a psychodynamic framework for understanding the causes of mental distress but described the nursing interventions in terms of supporting a medical model of care. Nursing care is dominated by a medical model which constrains mental health nursing. This potentially creates tension between what nurses believe to be the problem and the responses available for nurses in their clinical setting. A range of psychosocial approaches to mental health care delivery have been developed, but there seems to be problems with their implementation in practice. Further research is required to explore how broader therapeutic interventions can be implemented by nurses within multidisciplinary systems of mental health care delivery.
Meta‐barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity
Authors: ANDERSEN KENNETH , BIRD KAREN LISE , RASMUSSEN MORTEN , HAILE JAMES , BREUNING‐MADSEN HENRIK , KJÆR KURT H. , ORLANDO LUDOVIC , GILBERT M. THOMAS P. , WILLERSLEV ESKE 
Published: September 2011

AbstractDNA molecules originating from animals and plants can be retrieved directly from sediments and have been used for reconstructing both contemporary and past ecosystems. However, the extent to which such ‘dirt’ DNA reflects taxonomic richness and structural diversity remains contentious. Here, we couple second generation high‐throughput sequencing with 16S mitochondrial DNA (mtDNA) meta‐barcoding, to explore the accuracy and sensitivity of ‘dirt’ DNA as an indicator of vertebrate diversity, from soil sampled at safari parks, zoological gardens and farms with known species compositions. PCR amplification was successful in the full pH range of the investigated soils (6.2 ± 0.2 to 8.3 ± 0.2), but inhibition was detected in extracts from soil of high organic content. DNA movement (leaching) through strata was evident in some sporadic cases and is influenced by soil texture and structure. We find that DNA from the soil surface reflects overall taxonomic richness and relative biomass of individual species. However, one species that was recently introduced was not detected. Furthermore, animal behaviour was shown to influence DNA deposition rates. The approach potentially provides a quick methodological alternative to classical ecological surveys of biodiversity, and most reliable results are obtained with spatial sample replicates, while relative amounts of soil processed per site is of less importance.
The Contribution of NT‐gp96 as an Adjuvant for Increasing HPV16 E7‐Specific Immunity in C57BL /6 Mouse Model
Authors: Mohit E. , Bolhassani A. , Zahedifard F. , Taslimi Y. , Rafati S. 
Published: September 2011

AbstractTo control cervical cancer, efficient vaccination against human papillomavirus (HPV) is highly required. Despite the advantages and safety of the protein vaccines, additional strategies to enhance their immunogenicity are needed. E7 is a transforming protein which represents a perfect target antigen for vaccines or immunotherapies. Heat shock proteins (HSPs) facilitate cellular immune responses to antigenic peptides or proteins bound to them. Regarding to previous studies, vaccination with purified HSP/antigen complexes efficiently elicit antigen‐specific immune responses in mice model. The N‐terminal of glycoprotein 96 (NT‐gp96) has adjuvant effect and can induce effective cumulative immune response against clinical disorders, especially cancers. In this study, the recombinant HPV16 E7 and E7 linked to NT‐gp96 (E7‐NT‐gp96) proteins were generated in prokaryotic expression system. Mice were vaccinated twice with this recombinant proteins and the immunogenicity of the fusion protein was determined. The preventive efficacy of E7‐NT‐gp96 fusion protein was also evaluated and compared to E7 protein after challenging with cancerous TC‐1 cell line.In vitrore‐stimulated splenocytes of mice vaccinated with rE7‐NT‐gp96 protein induced higher IFN‐γ response in comparison with E7 protein immunization. Moreover, immunization with E7‐NT‐gp96 protein displayed low but stable humoral responses at post‐challenge time. The data showed that vaccination with fused E7‐NT‐gp96 protein delayed the tumour occurrence and growth as compared to protein E7 alone. These results suggest that fused adjuvant‐free E7‐NT‐gp96 protein vaccination could direct the immune responses towards Th1 immunity. Furthermore, the linkage of NT‐gp96 to E7 could enhance protective anti‐tumour immunity.