bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of implementation techniques for Galerkin projection between different meshes
Authors: Wang Z. , Henneron T. , Dular P. , Mipo J‐C. , Piriou F. 
Published: December 2013

AbstractTo solve multiphysics problems, weak coupling of finite element calculations can be carried out: the subproblems of which the physical nature differs are solved separately on their own meshes. In this case, Galerkin projection provides useful tool to ensure the transfer of physical fields between different meshes. In terms of implementation, the Galerkin projection system can be either accurately assembled over the intersection of two meshes or approximately integrated over the target mesh. This paper describes and compares these two implementation techniques for the Galerkin projection. Copyright © 2013 John Wiley & Sons, Ltd.
A reconstruction of the Asia‐Pacific Oscillation Index for the past 1500 years and its association with the Asian summer monsoon
Authors: Fang Keyan , Davi Nicole , D'Arrigo Rosanne 
Published: December 2013

ABSTRACTThere is a need to understand the long‐term variability Asian‐Pacific Oscillation (APO) due to its close linkages with large‐scale ocean–atmosphere anomalies. The first principal component (PC) of a network of 130 temperature proxies covering East Asia and the northeastern Pacific Ocean was employed to reconstruct the instrumental APO index from 500 to 2006. It explains 46.7% of the instrumental APO variance and correlates significantly with middle to upper tropospheric temperatures. The reconstructed APO reaches its peak in the Little Ice Age (LIA) and is low during the Medieval Climate Anomalies (MCA) period and since the 1850. The APO variations are caused by the temperature difference between East Asia and north Central Pacific Ocean. The Pacific Decadal Oscillations (PDOs) and tropical ocean‐atmospheric features [the El Niño–Southern Oscillation (ENSO) and the Indian Ocean Dipole (IOD)] are reversely connected to APO variations particularly on long timescale (e.g. centennial timescale) and short timescale (e.g. interannual), respectively, possibly via modulating the strength of the Asian summer monsoon. However, the relationship between the APO and both external forcings (e.g. solar irradiation) and the PDO are quite variable, which is significant only when the influences of the coupled ocean‐atmosphere patterns are weakened. The APO is positively correlated with indices of the hydroclimate of Monsoonal Asia, and is negatively associated with climatic indices for western North America.
Scaling up of Sustainable Land Management in the Western People's Republic of China: Evaluation of a 10‐Year Partnership
Authors: Tengberg Anna , Radstake Frank , Zhang Kebin , Dunn Bruce 
Published: December 2013

AbstractThe People's Republic of China‐Global Environment Facility Partnership to Combat Land Degradation in Dryland Ecosystems promotes an integrated ecosystem management (IEM) approach to restore, sustain and enhance the productive capacity of dryland ecosystems. This paper provides an analysis and synthesis of the funding strategies, methods and approaches that have been applied and tested under the Partnership to pilot and scale up IEM and sustainable land management (SLM) practices in the western People's Republic of China under its first 10 years. On the basis of a mix of methods using literature reviews, data collection at selected pilot sites through household questionnaire surveys, stakeholder workshops and field sampling, the following lessons were generated: (i) mainstreaming of IEM into relevant policy and development frameworks has been the most effective way of mobilizing funding for scaling up of SLM; (ii) SLM best practices need to be combined with economic incentives for land users, and pilot demonstrations of SLM need to be integrated into larger investment programmes to achieve impacts and economies of scale; (iii) market‐based approaches to scaling up of SLM, such as payment for ecosystem services and public–private partnerships, have a role to play, but cost–benefit analysis need to be better integrated into payment schemes; (iv) the economic benefits of carbon sequestration are too low to fund eco‐compensation schemes on their own but can provide supplementary funding; and (v) land degradation and SLM monitoring and assessment systems should be multiscale to support decision‐making on SLM and to monitor impact from the local to the national level. Copyright © 2014 Asian Development Bank
Subtilase SprP exerts pleiotropic effects inPseudomonas aeruginosa
Authors: Pelzer Alexander , Polen Tino , Funken Horst , Rosenau Frank , Wilhelm Susanne , Bott Michael , Jaeger Karl‐Erich 
Published: December 2013

AbstractThe open reading framePA1242in the genome ofPseudomonas aeruginosaPAO1 encodes a putative protease belonging to the peptidase S8 family of subtilases. The respective enzyme termed SprP consists of an N‐terminal signal peptide and a so‐called S8 domain linked by a domain of unknown function (DUF). Presumably, thisDUFdomain defines a discrete class ofPseudomonasproteins as homologous domains can be identified almost exclusively in proteins of the genusPseudomonas. ThesprPgene was expressed inEscherichia coliand proteolytic activity was demonstrated. AP. aeruginosa∆sprPmutant was constructed and its gene expression pattern compared to the wild‐type strain by genome microarray analysis revealing altered expression levels of 218 genes. Apparently, SprP is involved in regulation of a variety of different cellular processes inP. aeruginosaincluding pyoverdine synthesis, denitrification, the formation of cell aggregates, and of biofilms.
Alimentary, my dear Watson? The challenges of enteric α‐synuclein as a Parkinson's disease biomarker
Authors: Visanji Naomi P. , Marras Connie , Hazrati Lili‐Naz , Liu Louis W. C. , Lang Anthony E. 
Published: December 2013

ABSTRACTAn accurate early diagnostic test for Parkinson's disease (PD) is a critical unmet need. Recently, independent groups using different histological techniques have reported that the presence of alpha‐synuclein (α‐syn) in colonic biopsy tissue is able to distinguish living patients with PD from those without the disease. In addition, a further study has suggested that the presence of α‐syn in colonic biopsy tissue may be evident in early or even prodromal PD. However, several questions remain regarding the translation of these findings into using the assessment of α‐syn deposition in the enteric nervous system as a diagnostic biomarker for prodromal PD. Here we address critical issues related to the location and quantification of enteric α‐syn, detection of α‐syn with currently available histological techniques, timing of detection of α‐syn deposition, and, most crucially, whether enteric α‐syn can distinguish those with PD from both healthy individuals and individuals with other related diseases. We conclude that, although enteric α‐syn is a very exciting prospect, further studies will be vital to determine whether enteric α‐syn deposition has the potential to be the biomarker for prodromal PD that the field so desperately seeks. © 2013 International Parkinson and Movement Disorder Society
Genome‐wide association study in musician's dystonia: A risk variant at the arylsulfatase G locus?
Authors: Lohmann Katja , Schmidt Alexander , Schillert Arne , Winkler Susen , Albanese Alberto , Baas Frank , Bentivoglio Anna Rita , Borngräber Friederike , Brüggemann Norbert , Defazio Giovanni , Del Sorbo Francesca , Deuschl Günther , Edwards Mark J. , Gasser Thomas , Gómez‐Garre Pilar , Graf Julia , Groen Justus L. , Grünewald Anne , Hagenah Johann , Hemmelmann Claudia , Jabusch Hans‐Christian , Kaji Ryuji , Kasten Meike , Kawakami Hideshi , Kostic Vladimir S. , Liguori Maria , Mir Pablo , Münchau Alexander , Ricchiuti Felicia , Schreiber Stefan , Siegesmund Katharina , Svetel Marina , Tijssen Marina A.J. , Valente Enza Maria , Westenberger Ana , Zeuner Kirsten E. , Zittel Simone , Altenmüller Eckart , Ziegler Andreas , Klein Christine 
Published: December 2013

ABSTRACTMusician's dystonia (MD) affects 1% to 2% of professional musicians and frequently terminates performance careers. It is characterized by loss of voluntary motor control when playing the instrument. Little is known about genetic risk factors, although MD or writer's dystonia (WD) occurs in relatives of 20% of MD patients. We conducted a 2‐stage genome‐wide association study in whites. Genotypes at 557,620 single‐nucleotide polymorphisms (SNPs) passed stringent quality control for 127 patients and 984 controls. Ten SNPs revealed P < 10−5 and entered the replication phase including 116 MD patients and 125 healthy musicians. A genome‐wide significant SNP (P < 5 × 10−8) was also genotyped in 208 German or Dutch WD patients, 1,969 Caucasian, Spanish, and Japanese patients with other forms of focal or segmental dystonia as well as in 2,233 ethnically matched controls. Genome‐wide significance with MD was observed for an intronic variant in the arylsulfatase G (ARSG) gene (rs11655081; P = 3.95 × 10−9; odds ratio [OR], 4.33; 95% confidence interval [CI], 2.66‐7.05). rs11655081 was also associated with WD (P = 2.78 × 10−2) but not with any other focal or segmental dystonia. The allele frequency of rs11655081 varies substantially between different populations. The population stratification in our sample was modest (λ = 1.07), but the effect size may be overestimated. Using a small but homogenous patient sample, we provide data for a possible association of ARSG with MD. The variant may also contribute to the risk of WD, a form of dystonia that is often found in relatives of MD patients. © 2013 International Parkinson and Movement Disorder Society
EMILIN2 down‐modulates the Wnt signalling pathway and suppresses breast cancer cell growth and migration
Authors: Marastoni Stefano , Andreuzzi Eva , Paulitti Alice , Colladel Roberta , Pellicani Rosanna , Todaro Federico , Schiavinato Alvise , Bonaldo Paolo , Colombatti Alfonso , Mongiat Maurizio 
Published: December 2013

AbstractEMILIN2 is an extracellular matrix (ECM) protein that exerts contradictory effects within the tumour microenvironment: it induces apoptosis in a number of tumour cells, but it also enhances tumour neo‐angiogenesis. In this study, we describe a new mechanism by which EMILIN2 attenuates tumour cell viability. Based on sequence homology with the cysteine‐rich domain (CRD) of the Frizzled receptors, we hypothesized that EMILIN2 could affect Wnt signalling activation and demonstrate direct interaction with the Wnt1 ligand. This physical binding leads to decreased LRP6 phosphorylation and to the down‐modulation of β‐catenin, TAZ and their target genes. As a consequence, EMILIN2 negatively affects the viability, migration and tumourigenic potential of MDA‐MB‐231 breast cancer cells in a number of two‐ and three‐dimensional in vitro assays. EMILIN2 does not modulate Wnt signalling downstream of the Wnt–Frizzled interaction, since it does not affect the activation of the pathway following treatment with the GSK3 inhibitors LiCl and CHIR99021. The interaction with Wnt1 and the subsequent biological effects require the presence of the EMI domain, as there is no effect with a deletion mutant lacking this domain. Moreover, in vivo experiments show that the ectopic expression of EMILIN2, as well as treatment with the recombinant protein, significantly reduce tumour growth and dissemination of cancer cells in nude mice. Accordingly, the tumour samples are characterized by a significant down‐regulation of the Wnt signalling pathway. Altogether, these findings provide further evidence of the complex regulations governed by EMILIN2 in the tumour microenvironment, and they identify a key extracellular regulator of the Wnt signalling pathway. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Proline‐rich acidic protein 1 (PRAP1) is a novel interacting partner of MAD1 and has a suppressive role in mitotic checkpoint signalling in hepatocellular carcinoma
Authors: Sze Karen Man‐Fong , Chu Glanice Kin‐Yan , Mak Queenie Ho‐Yan , Lee Joyce Man‐Fong , Ng Irene Oi‐Lin 
Published: December 2013

AbstractLoss of mitotic checkpoint of cells contributes to chromosomal instability and leads to carcinogenesis. Mitotic arrest deficient 1 (MAD1) is a key component in mitotic checkpoint signalling. In this study, we identified a novel MAD1 interacting partner, proline‐rich acidic protein 1 (PRAP1), using yeast‐two hybrid screening, and investigated its role in mitotic checkpoint signalling in hepatocellular carcinoma (HCC). We demonstrated the physical interaction of PRAP1 with MAD1 and of PRAP1 with MAD1 isoform MAD1β, using a co‐immunoprecipitation assay. Moreover, stable expression of PRAP1 in mitotic checkpoint‐competent HCC cells, BEL‐7402 and SMMC‐7721, induced impairment of the mitotic checkpoint (p < 0.01), formation of chromosome bridges (p < 0.01) and aberrant chromosome numbers (p < 0.001). Interestingly, ectopic expression PRAP1 in HCC cells led to significant under‐expression of MAD1. In human HCC tumours, 40.4% (23/57) of HCCs showed under‐expression of PRAP1 protein as compared with their corresponding non‐tumorous livers; up‐regulation of MAD1 protein was significantly associated with down‐regulation of PRAP1 (p = 0.030). Our data revealed that PRAP1 is a protein interacting partner of MAD1 and that PRAP1 is able to down‐regulate MAD1 and suppress mitotic checkpoint signalling in HCC. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk
Signatures of n→π* interactions in proteins
Authors: Newberry Robert W. , Bartlett Gail J. , VanVeller Brett , Woolfson Derek N. , Raines Ronald T. 
Published: December 2013

AbstractThe folding of proteins is directed by a variety of interactions, including hydrogen bonding, electrostatics, van der Waals' interactions, and the hydrophobic effect. We have argued previously that an n→π* interaction between carbonyl groups be added to this list. In an n→π* interaction, the lone pair (n) of one carbonyl oxygen overlaps with the π* antibonding orbital of another carbonyl group. The tendency of backbone carbonyl groups in proteins to engage in this interaction has consequences for the structures of folded proteins that we unveil herein. First, we employ density functional theory to demonstrate that the n→π* interaction causes the carbonyl carbon to deviate from planarity. Then, we detect this signature of the n→π* interaction in high‐resolution structures of proteins. Finally, we demonstrate through natural population analysis that the n→π* interaction causes polarization of the electron density in carbonyl groups and detect that polarization in the electron density map of cholesterol oxidase, further validating the existence of n→π* interactions. We conclude that the n→π* interaction is operative in folded proteins.
Resistance to antibiotics targeted to the bacterial cell wall
Authors: Nikolaidis I. , Favini‐Stabile S. , Dessen A. 
Published: December 2013

AbstractPeptidoglycan is the main component of the bacterial cell wall. It is a complex, three‐dimensional mesh that surrounds the entire cell and is composed of strands of alternating glycan units crosslinked by short peptides. Its biosynthetic machinery has been, for the past five decades, a preferred target for the discovery of antibacterials. Synthesis of the peptidoglycan occurs sequentially within three cellular compartments (cytoplasm, membrane, and periplasm), and inhibitors of proteins that catalyze each stage have been identified, although not all are applicable for clinical use. A number of these antimicrobials, however, have been rendered inactive by resistance mechanisms. The employment of structural biology techniques has been instrumental in the understanding of such processes, as well as the development of strategies to overcome them. This review provides an overview of resistance mechanisms developed toward antibiotics that target bacterial cell wall precursors and its biosynthetic machinery. Strategies toward the development of novel inhibitors that could overcome resistance are also discussed.
Psychological Resilience, Affective Mechanisms and Symptom Burden in a Tertiary‐care Sample of Patients with Fibromyalgia
Authors: McAllister Samantha J. , Vincent Ann , Hassett Afton L. , Whipple Mary O. , Oh Terry H. , Benzo Roberto P. , Toussaint Loren L. 
Published: December 2013

AbstractResearch demonstrates that patients with fibromyalgia who have higher positive and lower negative affect have lower symptom burden. Affect has been shown to be associated with resilience. This study examined the relationship between affect, resilience and fibromyalgia symptom burden in a clinical sample of patients with fibromyalgia. We hypothesized that (a) positive and negative affect would be associated with fibromyalgia symptom burden; (b) resilience would be associated with positive and negative affect; (c) resilience would be associated with fibromyalgia symptom burden; and (d) the connection between resilience and fibromyalgia symptom burden would be mediated by both positive and negative affect. A sample of 858 patients with fibromyalgia completed questionnaires. Mediation modelling revealed statistically significant direct effects of resilience on fibromyalgia symptom burden (β = −0.10, P < 0.001) and statistically significant indirect effects of resilience on fibromyalgia symptom burden through affect (β = −0.36, P < 0.001), suggesting that both resilience and affect influence fibromyalgia symptom burden. Our results suggest that improving affect through resiliency training could be studied as a modality for improving fibromyalgia symptom burden. Copyright © 2013 John Wiley & Sons, Ltd.
Simplicity‐first model‐based plug‐in development
Authors: Naujokat Stefan , Neubauer Johannes , Lamprecht Anna‐Lena , Steffen Bernhard , Jörges Sven , Margaria Tiziana 
Published: December 2013

SUMMARYIn this article, we present our experience with over a decade of strict simplicity orientation in the development and evolution of plug‐ins. The point of our approach is to enable our graphical modeling framework jABC to capture plug‐in development in a domain‐specific setting. The typically quite tedious and technical plug‐in development is shifted this way from a programming task to the modeling level, where it can be mastered also by application experts without programming expertise. We show how the classical plug‐in development profits from a systematic domain‐specific API design and how the level of abstraction achieved this way can be further enhanced by defining adequate building blocks for high‐level plug‐in modeling. As the resulting plug‐in models can be compiled and deployed automatically, our approach decomposes plug‐in development into three phases where only the realization phase requires plug‐in‐specific effort. By using our modeling framework jABC, this effort boils down to graphical, tool‐supported process modeling. Furthermore, we support the automatic completion of process sketches for executability. All this will be illustrated along the most recent plug‐in‐based evolution of the jABC framework, which witnessed quite some bootstrapping effects. Copyright © 2013 John Wiley & Sons, Ltd.
Pylorus‐Resecting Pancreaticoduodenectomy Offers Long‐Term Outcomes Similar to Those of Pylorus‐Preserving Pancreaticoduodenectomy: Results of a Prospective Study
Authors: Kawai Manabu , Tani Masaji , Hirono Seiko , Okada Ken‐ichi , Miyazawa Motoki , Yamaue Hiroki 
Published: December 2013

AbstractBackground
We showed in a previous study that pylorus‐resecting pancreaticoduodenectomy (PrPD), which divides the stomach adjacent to the pylorus ring, preserves more than 95 % of the stomach and significantly reduced the incidence of delayed gastric emptying (DGE) compared with pylorus‐preserving pancreaticoduodenectomy (PpPD). However, long‐term outcomes of PrPD and the adverse effect of early postoperative DGE on long‐term outcomes remain unclear.MethodsA total of 130 patients enrolled in a previous study were followed for 24 months after surgery. Primary endpoint was whether PrPD is a better surgical procedure than PpPD regarding long‐term outcomes.ResultsWeight loss > grade 2 (Common Terminology Criteria for Adverse Events, Version 4.03) at 24 months after surgery was significantly better in group PrPD (16.2 %) than in group PpPD (42.2 %) (p = 0.011). Nutritional status and late postoperative complications were similar for the two groups. The incidence of weight loss > grade 2 at 24 months was 63.6 % in DGE patients with DGE and 25.3 % in non‐DGE patients (p = 0.010). Tmax (time to peak 13CO2 content in 13C‐acetate breath test) at 24 months in DGE patients was significantly delayed compared with that in non‐DGE patients (27.9 ± 22.7 vs. 16.5 ± 10.1 min, p = 0.023). Serum albumin level at 24 months was higher in non‐DGE patients than in those with DGE (3.7 ± 0.6 vs. 4.1 ± 0.4 g/dl, p = 0.013).ConclusionsPrPD offers long‐term outcomes similar to those of PpPD. DGE may be associated with weight loss and poor nutritional status in patients with long‐term outcomes.
Enhancing Surgical Performance Outcomes Through Process‐driven Care: A Systematic Review
Authors: Pucher Philip H. , Aggarwal Rajesh , Singh Pritam , Darzi Ara 
Published: December 2013

AbstractBackgroundRecent evidence has demonstrated the variability in quality of postoperative care, as measured by rates of failure to rescue (FTR). The identification of structure‐ and process‐related factors affecting the quality of postoperative care is the first step towards understanding and improving outcomes. The aim of this review is to review current evidence for structure and process factors affecting postoperative care.MethodsA systematic review was conducted. Studies were selected that examined structure or process variables affecting FTR rates and postoperative outcomes. Quality analysis with Jadad and Newcastle–Ottawa scales was conducted and poor‐quality studies were excluded.ResultsThirty‐seven studies were included in final analysis. Of these, 23 were related to enhanced recovery protocols in seven surgical specialties. Twenty‐one of these 23 studies reported decreases in length of stay. Six studies also reported decreases in morbidity. No studies reported increases in stay duration or morbidity. Of the 16 studies that examined other structural and process factors, the strongest evidence was for the association between nursing ratios and FTR rates. The effects of hospital size, resources, and subspecialist care processes were less clear.ConclusionProcess‐led care represents a clear, evidence‐based approach that can be integrated on a local scale, without necessitating major structural or organisational change, to improve outcomes and may also be cost effective. To foster success, process improvement must be driven on a local level and backed up by appropriate understanding, education, and multidisciplinary involvement.