bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-eddy simulation of separation and reattachment of a flat plate turbulent boundary layer
Authors: Cheng W. , Pullin D. I. , Samtaney R. 
Published: November 2015

We present large-eddy simulations (LES) of separation and reattachment of a flat-plate turbulent boundary-layer flow. Instead of resolving the near wall region, we develop a two-dimensional virtual wall model which can calculate the time- and space-dependent skin-friction vector field at the wall, at the resolved scale. By combining the virtual-wall model with the stretched-vortex subgrid-scale (SGS) model, we construct a self-consistent framework for the LES of separating and reattaching turbulent wall-bounded flows at large Reynolds numbers. The present LES methodology is applied to two different experimental flows designed to produce separation/reattachment of a flat-plate turbulent boundary layer at medium Reynolds number $Re_{{\it\theta}}$ based on the momentum boundary-layer thickness ${\it\theta}$. Comparison with data from the first case at $Re_{{\it\theta}}=2000$ demonstrates the present capability for accurate calculation of the variation, with the streamwise co-ordinate up to separation, of the skin friction coefficient, $Re_{{\it\theta}}$, the boundary-layer shape factor and a non-dimensional pressure-gradient parameter. Additionally the main large-scale features of the separation bubble, including the mean streamwise velocity profiles, show good agreement with experiment. At the larger $Re_{{\it\theta}}=11\,000$ of the second case, the LES provides good postdiction of the measured skin-friction variation along the whole streamwise extent of the experiment, consisting of a very strong adverse pressure gradient leading to separation within the separation bubble itself, and in the recovering or reattachment region of strongly-favourable pressure gradient. Overall, the present two-dimensional wall model used in LES appears to be capable of capturing the quantitative features of a separation-reattachment turbulent boundary-layer flow at low to moderately large Reynolds numbers.
Inflammatory potential of diet and risk for hepatocellular cancer in a case–control study from Italy
Authors: Shivappa Nitin , Hébert James R. , Polesel Jerry , Zucchetto Antonella , Crispo Anna , Montella Maurizio , Franceschi Silvia , Rossi Marta , La Vecchia Carlo , Serraino Diego 
Published: November 2015

AbstractInflammation and diet have been suggested to be important risk factors for hepatocellular cancer (HCC). This Italian multicentre hospital-based case–control study conducted between 1999 and 2002 and including 185 cases with incident, histologically confirmed HCC, and 404 controls hospitalised for acute non-neoplastic diseases provided an opportunity to investigate the association between HCC and the dietary inflammatory index (DII). The DII was computed on the basis of dietary intake assessed 2 years before the date of interview by a validated sixty-three-item FFQ. Logistic regression models were used to estimate OR adjusted for age, sex, study centre, education, BMI, smoking, physical activity, serum markers of hepatitis B and C infection and energy intake. Energy adjustment for DII was performed using the residual method. Participants in the highest tertile of DII scores (i.e. with a more pro-inflammatory diet) had a higher risk for HCC (ORtertile 3 v, 1 2·43; 95 % CI 1·27, 4·68; Ptrend=0·03). When stratified by the presence or absence of hepatitis B/C infection and sex, DII was strongly associated with HCC in hepatitis B- and C-negative participants (ORtertile 3 v. 1 4·18; 95 % CI 1·53, 11·39; Ptrend=0·02) and among males (ORtertile 3 v. 1 3·60; 95 % CI 1·65, 7·87; Ptrend=0·001). These results indicate that a pro-inflammatory diet is associated with increased risk for HCC, in those without a history of hepatitis B/C infection and among males.
Volterra, Fascism, and France
Authors: Capristo Annalisa 
Published: November 2015

ArgumentMy contribution focuses on two aspects strictly related each other. On one hand, the progressive marginalization of Volterra from Italian scientific and political life after the rise of Fascism – because of his public anti-Fascist stance, both as a senator and as a professor – until his definitive exclusion on racial grounds in 1938. On the other hand, the reactions of his French colleagues and friends to this ostracism, and the support he received from them. As it emerges from several sources (Volterra's correspondence, institutional documentation, conference proceedings, etc.), it was mainly thanks to their support that he was able to escape the complete isolation and the “civil death” to which the regime condemned many of its adversaries.
Polemics in Public: Poncelet, Gergonne, Plücker, and the Duality Controversy
Authors: Lorenat Jemma 
Published: November 2015

ArgumentA plagiarism charge in 1827 sparked a public controversy centered between Jean-Victor Poncelet (1788–1867) and Joseph-Diez Gergonne (1771–1859) over the origin and applications of the principle of duality in geometry. Over the next three years and through the pages of various journals, monographs, letters, reviews, reports, and footnotes, vitriol between the antagonists increased as their potential publicity grew. While the historical literature offers valuable resources toward understanding the development, content, and applications of geometric duality, the hostile nature of the exchange seems to have deterred an in-depth textual study of the explicitly polemical writings. We argue that the necessary collective endeavor of beginning and ending this controversy constitutes a case study in the circulation of geometry. In particular, we consider how the duality controversy functioned as a medium of communicating new fundamental principles to a wider audience of practitioners.
Models of Temporal Discounting 1937–2000: An Interdisciplinary Exchange between Economics and Psychology
Authors: Grüne-Yanoff Till 
Published: November 2015

ArgumentToday's models of temporal discounting are the result of multiple interdisciplinary exchanges between psychology and economics. Although these exchanges did not result in an integrated discipline, they had important effects on all disciplines involved. The paper describes these exchanges from the 1930s onwards, focusing on two episodes in particular: an attempted synthesis by psychiatrist George Ainslie and others in the 1970s; and the attempted application of this new discounting model by a generation of economists and psychologists in the 1980s, which ultimately ended in thediversity of measurements disappointment. I draw four main conclusions. First, multiple notions of temporal discounting must be conceptually distinguished. Second, behavioral economics is not an integration or unification of psychology and economics. Third, the analysis identifies some central disciplinary markers that distinguish modeling strategies in economics and psychology. Finally, it offers a case of interdisciplinary success that does not fit the currently dominant account of interdisciplinarity as integration.
The Ontology of Determination: From Descartes to Spinoza
Authors: Sangiacomo Andrea 
Published: November 2015

ArgumentThis paper argues that Spinoza's notions of “conatus” and “power of acting” are derived by means of generalization from the notions of “force of motion” and “force of determination” that Spinoza discussed in hisPrinciples of Cartesian Philosophyto account for interactions among bodies (impacts) on the basis of their degrees of contrariety. I argue that in theEthics, Spinoza's ontology entails that interactions must always be accounted for in terms of degrees of “agreement or disagreement in nature” among interacting things. The notion of “power of acting” is used to express the extent to which a thing's conatus is aided or restrained by external causes on the basis of its degree of agreement or disagreement in nature with them. “Power of acting” generalizes the same approach and method of resolution at the basis of the notion of “force of determination” in order to account for causal interactions not only among the simplest bodies but also among more complex individuals.
Disease burden of congenital cytomegalovirus infection at school entry age: study design, participation rate and birth prevalence
Authors: KORNDEWAL M. J. , VOSSEN A. C. T. M. , CREMER J. , VAN BINNENDIJK R. S. , KROES A. C. M. , VAN DER SANDE M. A. B. , OUDESLUYS-MURPHY A. M. , DE MELKER H. E. 
Published: November 2015

SUMMARYCongenital cytomegalovirus infection (cCMV) may lead to symptoms at birth and long-term consequences. We present a nationwide, retrospective cohort study on the outcome of cCMV up to age 6 years. For this study we identified cCMV, using polymerase chain reaction, by analysing dried blood spots, which are taken shortly after birth for neonatal screening. The group of children with cCMV were compared to a group of children who were cCMV negative at birth. Data were collected about their health and development up to age 6 years. Parents of 73 693 children were invited to participate, and 32 486 (44·1%) gave informed consent for testing of their child's dried blood spot for CMV. Of the 31 484 dried blood spots tested, 156 (0·5%) were positive for cCMV. Of these, four (2·6%) children had been diagnosed with cCMV prior to this study. This unique retrospective nationwide study permits the estimation of long-term sequelae of cCMV up to the age of 6 years. The birth prevalence of cCMV in this study was 0·5%, which is in line with prior estimates. Most (97·4%) children with cCMV had not been diagnosed earlier, indicating under-diagnosis of cCMV.
Hypertrophic cardiomyopathy in Donohue syndrome
Authors: Termote Jacqueline U. M. , Breur Johannes M. P. J. , de Vroede Monique A. M. J. 
Published: November 2015

AbstractWe report the case of a patient with Donohue syndrome who died of heart failure due to obstructive hypertrophic cardiomyopathy. A literature survey revealed that hypertrophic cardiomyopathy was present in 30% of these patients and was often fatal. Therefore, every patient with Donohue syndrome should be screened for hypertrophic cardiomyopathy.
Translating text into pictographs
Authors: VANDEGHINSTE VINCENT , SEVENS INEKE SCHUURMAN LEEN , VAN EYNDE FRANK 
Published: November 2015

AbstractWe describe and evaluate a text-to-pictograph translation system that is used in an online platform for Augmentative and Alternative Communication, which is intended for people who are not able to read and write, but who still want to communicate with the outside world. The system is set up to translate from Dutch into Sclera and Beta, two publicly available pictograph sets consisting of several thousands of pictographs each. We have linked large amounts of these pictographs to synsets or combinations of synsets of Cornetto, a lexical-semantic database for Dutch similar to WordNet. In the translation system, the Dutch input text undergoes shallow linguistic analysis and the synsets of the content words are looked up. The system looks for the nearest pictographs in the lexical-semantic database and displays the message into pictographs. We evaluated the system and results showed a large improvement over the baseline system which consisted of straightforward string-matching between the input text and the filenames of the pictographs.Our system provides a clear improvement in the communication possibilities of illiterate people. Nevertheless there is room for further improvement.
PDLIM7 is a novel target of the ubiquitin ligase Nedd4-1 in skeletal muscle
Authors: D'Cruz Robert , Plant Pamela J. , Pablo Lesley A. , Lin Shouzhe , Chackowicz Joshua , Correa Judy , Bain James , Batt Jane 
Published: November 2015

Skeletal muscle atrophy remains a complication occurring both as a natural response to muscle disuse and as a pathophysiological response to illness such as diabetes mellitus and nerve injury, such as traumatic muscle denervation. The ubiquitin–proteasome system (UPS) is the predominant proteolytic machinery responsible for atrophy of skeletal muscle, and Nedd4-1 (neural precursor cell-expressed developmentally down-regulated 4-1) is one of a series of E3 ubiquitin ligases identified to mediate inactivity-induced muscle wasting. Targets of Nedd4-1 mediated ubiquitination in skeletal muscle remain poorly understood. In the present study, we identified PDLIM7 (PDZ and LIM domain 7, Enigma), a member of the PDZ–LIM family of proteins, as a novel target of Nedd4-1 in skeletal muscle. The PDZ–LIM family of proteins is known to regulate muscle development and function. We show that Nedd4-1 expression in muscle atrophied by denervation is co-incident with a decrease in PDLIM7 and that PDLIM7 protein levels are stabilized in denervated muscle of Nedd4-1 skeletal muscle-specific knockout mice (SMS-KO). Exogenous PDLIM7 and Nedd4-1 transfected into human embryonic kidney (HEK)293 cells co-immunoprecipitate through binding between the PY motif of PDLIM7 and the second and third WW domains of Nedd4-1 and endogenous PDLIM7 and Nedd4-1 interact in the cytoplasm of differentiated C2C12 myotubes, leading to PDLIM7 ubiquitination. These results identify PDLIM7 as a bona fide skeletal muscle substrate of Nedd4-1 and suggest that this interaction may underlie the progression of skeletal muscle atrophy. This offers a novel therapeutic target that could be potentially used to attenuate muscle atrophy.
Plasma-derived and synthetic high-density lipoprotein inhibit tissue factor in endothelial cells and monocytes
Authors: Ossoli Alice , Remaley Alan T. , Vaisman Boris , Calabresi Laura , Gomaraschi Monica 
Published: November 2015

HDL (high-density lipoproteins) exert anti-thrombotic activities by preventing platelet adhesion and activation and by stimulating the protein C pathway and fibrinolysis. The aim of the present study was to assess the effect of plasma-derived and synthetic HDL on endothelial and monocyte expression of TF (tissue factor), the primary initiator of coagulation. HDL inhibited TF expression and activity in stimulated endothelial cells and monocytes in a dose-dependent way. Synthetic HDL fully retain the ability to inhibit TF expression in a dose-dependent manner; lipid-free apoA-I (apolipoprotein A-I) was not effective and neither was sphingosine 1-phosphate involved. HDL-mediated TF inhibition was due to a modulation of cellular cholesterol content through the interaction with SR-BI (scavenger receptor BI); downstream, HDL inhibited the activation of p38 MAPK (mitogen-activated protein kinase) and the repression of the PI3K (phosphoinositide 3-kinase) pathway responsible for TF expression. In vivo, human apoA-I-transgenic mice displayed a reduced aortic TF expression compared with wild-type animals and TF plasma levels were increased in subjects with low HDL-C (HDL-cholesterol) levels compared with high HDL-C subjects. Thus the anti-thrombotic activity of HDL could also be mediated by the inhibition of TF expression and activity in endothelial cells and monocytes; synthetic HDL retain the inhibitory activity of plasma-derived HDL, supporting the hypothesis that synthetic HDL infusion may be beneficial in the setting of acute coronary syndrome.
Estuarine Residency and Migration of Southern Flounder Inferred from Conventional Tag Returns at Multiple Spatial Scales
Authors: Craig J. Kevin , Smith William E. , Scharf Frederick S. , Monaghan James P. 
Published: November 2015

Abstract
An improved understanding of the spatial structure and movements of harvested populations can promote more efficient management of marine resources. Conventional tagging is a valuable approach to study the movements of marine fishes due to its relatively low expense and the typically broad spatial extent over which movements can be characterized. We present the findings of multiple tag return studies initiated in the estuaries of North Carolina during the past two decades to better understand habitat residency and migration patterns of Southern Flounder Paralichthys lethostigma, an economically important marine flatfish in the southeastern USA. Tag return data indicated large-scale (&gt;50 km) movements of relatively large fish in the fall, which were presumably associated with offshore winter spawning migrations. Nearly all Southern Flounder that demonstrated large-scale movement were recovered to the south of the system in which they were tagged, suggesting that the spawning activity of fish using North Carolina estuaries may be concentrated mostly off the southeastern U.S. continental shelf. Tag returns from within multiple estuarine systems during the spring and summer were in close proximity to release sites (typically &lt; 1 km), suggesting limited movement during estuarine residency. Recaptures in the spring of fish tagged the previous summer or fall were also in close proximity to release sites, in some cases within the same estuarine creek, indicating limited movement of fish overwintering in the estuary as well. Our findings reveal saltatory movement dynamics of Southern Flounder characterized by limited movement during estuarine residency and large-scale movements in the fall associated with spawning migrations. Our synthesis of several tag return studies across multiple spatial scales should contribute to a better alignment of Southern Flounder management with their spatial dynamics.
Received April 13, 2015; accepted July 20, 2015
Comparisons of the reference measuring instruments of surface parameters
Authors: Kupko Vladimir , Lysenko Valeriy 
Published: November 2015

A bilateral comparison of measurements on a Type A1 roughness standard has been undertaken between metrology institutes in Ukraine and Russia. The measurand was the parameter R
max, located on two different sections of the artefact with nominal values of 0.250 μm and 49 μm. The results of the two participants are in agreement within the combined uncertainties, thus equivalence of the measurements is demonstrated.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCL, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Key comparison BIPM.RI(I)-K1 of the air-kerma standards of the ENEA-INMRI, Italy and the BIPM in 60Co gamma radiation
Authors: Kessler C , Pinto M , Cappadozzi G , Silvestri C , Bovi M , Toni M P 
Published: November 2015

A direct comparison of the standards for air kerma of the Istituto Nazionale di Metrologia delle Radiazioni Ionizzanti (ENEA-INMRI), Italy and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in June 2015. The comparison result, evaluated as a ratio of the ENEA and the BIPM standards for air kerma, is 0.9999 with a combined standard uncertainty of 2.2 × 10−3. The results are analysed and presented in terms of degrees of equivalence for entry in the BIPM key comparison database.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes
Authors: Steinrücken Matthias , Jewett Ethan M. , Song Yun S. 
Published: November 2015

Abstract
Motivation: In the Wright–Fisher diffusion, the transition density function describes the time evolution of the population-wide frequency of an allele. This function has several practical applications in population genetics and computing it for biologically realistic scenarios with selection and demography is an important problem.
Results: We develop an efficient method for finding a spectral representation of the transition density function for a general model where the effective population size, selection coefficients and mutation parameters vary over time in a piecewise constant manner.
Availability and implementation: The method, called SpectralTDF, is available at https://sourceforge.net/projects/spectraltdf/.
Contact: yss@berkeley.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Flexible data integration and curation using a graph-based approach
Authors: Croset Samuel , Rupp Joachim , Romacker Martin 
Published: November 2015

Abstract
Motivation: The increasing diversity of data available to the biomedical scientist holds promise for better understanding of diseases and discovery of new treatments for patients. In order to provide a complete picture of a biomedical question, data from many different origins needs to be combined into a unified representation. During this data integration process, inevitable errors and ambiguities present in the initial sources compromise the quality of the resulting data warehouse, and greatly diminish the scientific value of the content. Expensive and time-consuming manual curation is then required to improve the quality of the information. However, it becomes increasingly difficult to dedicate and optimize the resources for data integration projects as available repositories are growing both in size and in number everyday.
Results: We present a new generic methodology to identify problematic records, causing what we describe as ‘data hairball’ structures. The approach is graph-based and relies on two metrics traditionally used in social sciences: the graph density and the betweenness centrality. We evaluate and discuss these measures and show their relevance for flexible, optimized and automated data curation and linkage. The methodology focuses on information coherence and correctness to improve the scientific meaningfulness of data integration endeavors, such as knowledge bases and large data warehouses.
Contact: samuel.croset@roche.com
Supplementary information: Supplementary data are available at Bioinformatics online.
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments
Authors: Thomas Brandon R. , Chylek Lily A. , Colvin Joshua , Sirimulla Suman , Clayton Andrew H.A. , Hlavacek William S. , Posner Richard G. 
Published: November 2015

Abstract
Summary: Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.
Availability and implementation: BioNetFit can be used on stand-alone Mac, Windows/Cygwin, and Linux platforms and on Linux-based clusters running SLURM, Torque/PBS, or SGE. The BioNetFit source code (Perl) is freely available (http://bionetfit.nau.edu).
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: bionetgen.help@gmail.com