bluuebunny/crossref_metadata_2025_split huggingface dataset:
Academics and competing interests in H1N1 influenza media reporting
Authors: Mandeville Kate L , O'Neill Sam , Brighouse Andrew , Walker Alice , Yarrow Kielan , Chan Kenneth 
Published: November 2013

BackgroundConcerns have been raised over competing interests (CoI) among academics during the 2009 to 2010 A/H1N1 pandemic. Media reporting can influence public anxiety and demand for pharmaceutical products. We assessed CoI of academics providing media commentary during the early stages of the pandemic.MethodsWe performed a retrospective content analysis of UK newspaper articles on A/H1N1 influenza, examining quoted sources. We noted when academics made a risk assessment of the pandemic and compared this with official estimations. We also looked for promotion or rejection of the use of neuraminidase inhibitors or H1N1-specific vaccine. We independently searched for CoI for each academic.ResultsAcademics were the second most frequently quoted source after Ministers of Health. Where both academics and official agencies estimated the risk of H1N1, one in two academics assessed the risk as higher than official predictions. For academics with CoI, the odds of a higher risk assessment were 5.8 times greater than those made by academics without CoI (Wald p value=0.009). One in two academics commenting on the use of neuraminidase inhibitors or vaccine had CoI. The odds of CoI in academics promoting the use of neuraminidase inhibitors were 8.4 times greater than for academics not commenting on their use (Fisher's exact p=0.005).ConclusionsThere is evidence of CoI among academics providing media commentary during the early H1N1 pandemic. Heightened risk assessments, combined with advocacy for pharmaceutical products to counter this risk, may lead to increased public anxiety and demand. Academics should declare, and journalists report, relevant CoI for media interviews.
CONSENSUS-LIKE ALGORITHMS FOR ESTIMATION OF GAUSSIAN MIXTURES OVER LARGE SCALE NETWORKS
Authors: FAGNANI FABIO , FOSSON SOPHIE M. , RAVAZZI CHIARA 
Published: November 2013

In this paper, we address the problem of estimating Gaussian mixtures in a sensor network. The scenario we consider is the following: a common signal is acquired by sensors, whose measurements are affected by standard Gaussian noise and by different offsets. The measurements can thus be statistically modeled as mixtures of Gaussians with equal variance and different expected values. The aim of the network is to achieve a common estimation of the signal, and to cluster the sensors according to their own offsets.For this purpose, we develop an iterative, distributed, consensus-like algorithm based on Maximum Likelihood estimation, which is well-suited to work in-network when the communication to a central processing unit is not allowed. Estimation is performed by the sensors themselves, which typically consist of devices with limited computational capabilities.Our main contribution is the analytical proof of the convergence of the algorithm. Our protocol is compared with existing methods via numerical simulations and the trade-offs between robustness, speed of convergence and implementation simplicity are discussed in detail.
The carbonate-evaporite lagoon of Al Dakhirah (Qatar): an example of a modern depositional model controlled by longshore transport
Authors: Billeaud Isabelle , Caline Bruno , Livas Benjamin , Tessier Bernadette , Davaud Eric , Frebourg Gregory , Hasler Claude-Alain , Laurier Dominique , Pabian-Goyheneche Cecile 
Published: November 2013

Abstract
The southern coast of the Arabian Gulf is considered a good example of an arid carbonate depositional system. The objective of this field investigation is to better elucidate the dynamic controls on the character and pattern of the depositional belts in a carbonate-evaporite lagoonal setting. The interpretation of this lagoon is based on combined field examination and laboratory analyses of surface samples, and this has resulted in an updated depositional model for carbonate-evaporite lagoonal settings. This study highlights the effects of sediment transport by longshore currents, with the formation of sand spits that gradually closed the lagoon during their southwards migration. The associated narrow and elongated back-barrier settings consist of tidal-dominated muddy sediments affected by a network of tidal channels. This wave-dominated high-energy system has generated several carbonate barrier and back-barrier units that migrated southwards and seawards during the last few thousands of years. This updated depositional model significantly differs from shoreline-parallel facies tracts of the classical Trucial Coast model, where the dominant wind is orientated perpendicular to the coastline. Conversely to the sediment belts of the Trucial Coast, the Al Dakhirah lagoon displays a strongly asymmetrical pattern of the sediment belts, marked by a southwards and seawards migration.
Stone uses in Reims Cathedral: provenance, physical properties and restoration phases
Authors: Turmel A. , Fronteau G. , Thomachot-Schneider C. , Moreau C. , Chalumeau L. , Barbin V. 
Published: November 2013

Abstract

Reims Cathedral is a major monument in the NE of France originally built with local Lutetian limestone. The recent closure of the last quarries has made restoration using the same stone more complicated. The restoration stones used currently are Lutetian limestones from the centre of the Paris Basin (Saint-Pierre-Aigle and Saint-Maximin stones). Mapping of the Cathedral's façades confirmed the data from ancient manuscripts: Courville stone was the original building stone, but several other local stones from various quarries and beds were also used. As a follow-up to this mapping, Lutetian limestones from five disused quarries were sampled for petrophysical characterization tests: thin section analyses, porosimetry, capillary and drying kinetics. The petrophysical properties of the limestones showed differences between the two main local stone types (
Ditrupa
limestone and miliolids limestone) and also between the quarries. This study addresses the difficulty of selecting new stone for restoration. Should ancient quarries be re-opened? If so, which ones?
Replacement stones for Lede stone in Belgian historical monuments
Authors: De Kock Tim , Dewanckele Jan , Boone Marijn , De Schutter Geert , Jacobs Patric , Cnudde Veerle 
Published: November 2013

Abstract
The Lede stone (Lutetian, Eocene) is an important historic building stone used in the NW of Belgium. In Ghent, it is dominant in the post-Romanesque built cultural heritage. Its use was restricted several times by socio-economic constraints. Since quarrying and production started to cease from the seventeenth century, periodic revivals favoured the use of Lede stone for new buildings and restoration projects. Sulphation is the main threat for the Lede stone as black crusts are the most common degradation phenomena on this arenaceous limestone. Around the turn of the nineteenth century, the Belgian Gobertange stone was the most widely used replacement material. Throughout the twentieth century, the use of replacement material shifted towards French limestones. However, their colour, texture and petrophysical properties differ from the Lede stone, for which a natural yellow–brown patina is very characteristic. In order to solve this mainly aesthetic issue, several new stone types are used as replacement stone in the twenty-first century, while many others have been suggested. It remains, however, difficult to find a replacement stone that matches the visual and petrophysical properties of the Lede stone. One remaining Lede stone quarry pit has increased its activity since 2011, offering the opportunity to use new Lede stone as replacement stone.
Probabilistic Relational Reasoning for Differential Privacy
Authors: Barthe Gilles , Köpf Boris , Olmedo Federico , Zanella-Béguelin Santiago 
Published: November 2013

Differential privacy is a notion of confidentiality that allows useful computations on sensible data while protecting the privacy of individuals. Proving differential privacy is a difficult and error-prone task that calls for principled approaches and tool support. Approaches based on linear types and static analysis have recently emerged; however, an increasing number of programs achieve privacy using techniques that fall out of their scope. Examples include programs that aim for weaker, approximate differential privacy guarantees and programs that achieve differential privacy without using any standard mechanisms. Providing support for reasoning about the privacy of such programs has been an open problem.
We report on CertiPriv, a machine-checked framework for reasoning about differential privacy built on top of the Coq proof assistant. The central component of CertiPriv is a quantitative extension of probabilistic relational Hoare logic that enables one to derive differential privacy guarantees for programs from first principles. We demonstrate the applicability of CertiPriv on a number of examples whose formal analysis is out of the reach of previous techniques. In particular, we provide the first machine-checked proofs of correctness of the Laplacian, Gaussian, and exponential mechanisms and of the privacy of randomized and streaming algorithms from the literature.
PIK3CA, BRAF, and PTEN Status and Benefit from Cetuximab in the Treatment of Advanced Colorectal Cancer—Results from NCIC CTG/AGITG CO.17
Authors: Karapetis Christos S. , Jonker Derek , Daneshmand Manijeh , Hanson Jennifer E. , O'Callaghan Christopher J. , Marginean Celia , Zalcberg John R. , Simes John , Moore Malcolm J. , Tebbutt Niall C. , Price Timothy J. , Shapiro Jeremy D. , Pavlakis Nick , Gibbs Peter , Van Hazel Guy A. , Lee Ursula , Haq Rashida , Virk Shakeel , Tu Dongsheng , Lorimer Ian A.J. ,   for the NCIC Clinical Trials Group and the Australasian Gastro-Intestinal Trials Group
Published: November 2013

Abstract
Purpose: Cetuximab improves survival in patients with K-ras wild-type advanced colorectal cancer. We examined the predictive and prognostic significance of additional biomarkers in this setting, in particular BRAF, PIK3CA, and PTEN.
Experimental Design: Available colorectal tumor samples were analyzed from the CO.17 study. BRAF mutations were identified in tumor-derived DNA by direct sequencing and PIK3CA mutations were identified using a high-resolution melting screen with confirmation by sequencing. PTEN expression by immunohistochemistry (IHC) was performed on tissue microarrays. For each biomarker, prognostic and predictive effects were examined using a Cox model with tests for treatment–biomarker interaction.
Results: A total of 572 patients with pretreated colorectal cancer were randomly assigned to receive cetuximab or best supportive care (BSC). Of 401 patients assessed for BRAF status, 13 (3.2%) had mutations. Of 407 patients assessed for PIK3CA status, 61 (15%) had mutations. Of 205 patients assessed for PTEN, 148 (72%) were negative for IHC expression. None of BRAF, PIK3CA, or PTEN was prognostic for overall or progression-free survival in the BSC arm. None was predictive of benefit from cetuximab, either in the whole study population or the K-ras wild-type subset. In the K-ras wild-type subgroup, the overall survival adjusted HR according to BRAF mutation status was 1.39 (interaction P = 0.69), PIK3CA mutation status HR = 0.79 (interaction P = 0.63), and PTEN expression HR = 0.75 (interaction P = 0.61).
Conclusions: In chemotherapy-refractory colorectal cancer, neither PIK3CA mutation status nor PTEN expression were prognostic, nor were they predictive of benefit from cetuximab. Evaluation of predictive significance of BRAF mutations requires a larger sample size. Clin Cancer Res; 20(3); 744–53. ©2013 AACR.
Long-lasting Disease Stabilization in the Absence of Toxicity in Metastatic Lung Cancer Patients Vaccinated with an Epitope Derived from Indoleamine 2,3 Dioxygenase
Authors: Iversen Trine Zeeberg , Engell-Noerregaard Lotte , Ellebaek Eva , Andersen Rikke , Larsen Stine Kiaer , Bjoern Jon , Zeyher Claus , Gouttefangeas Cécile , Thomsen Birthe Moerk , Holm Bente , thor Straten Per , Mellemgaard Anders , Andersen Mads Hald , Svane Inge Marie 
Published: November 2013

AbstractPurpose: To investigate targeting of indoleamine 2,3 dioxygenase (IDO) enzyme using a synthetic peptide vaccine administered to patients with metastatic non–small cell lung cancer (NSCLC).Experimental Design: In a clinical phase I study, we treated 15 HLA-A2–positive patients with stage III–IV NSCLC in disease stabilization after standard chemotherapy. Patients were treated with imiquimod ointment and subcutaneous vaccinations (100 μg IDO5 peptide, sequence ALLEIASCL, formulated in 900 μL Montanide). Primary endpoint was toxicity. Clinical benefit and immunity were assessed as secondary endpoints.Results: No severe toxicity was observed. One patient developed a partial response (PR) after one year of vaccine treatment, whereas long-lasting stable disease (SD) ≥ 8.5 months was demonstrated in another six patients. The median overall survival (OS) was 25.9 months. Patients demonstrated significant improved OS (P = 0.03) when compared with the group of patients excluded because of HLA-A2 negativity. IDO-specific CD8+ T-cell immunity was demonstrated by IFN-γ Elispot and Tetramer staining. Fluorescence-activated cell sorting analyses demonstrated a significant reduction of the Treg population (P = 0.03) after the sixth vaccine (2.5 months) compared with pretreatment levels. Furthermore, expression of IDO was detected in nine of ten tumor biopsies by immunohistochemistry. High-performance liquid chromatography analyses of kynurenine/tryptophan (Kyn/Trp) ratio in sera were performed. In long-term analyses of two clinical responding patients, the ratio of Kyn/Trp remained stable.Conclusions: The vaccine was well tolerated with no severe toxicity occurring. A median OS of 25.9 months was demonstrated and long-lasting PR+SD was seen in 47% of the patients. Clin Cancer Res; 20(1); 221–32. ©2013 AACR.
Did the 2007 Legal Arizona Workers Act Reduce the State's Unauthorized Immigrant Population?
Authors: Bohn Sarah , Lofstrom Magnus , Raphael Steven 
Published: November 2013

Abstract
We test for an effect of Arizona's 2007 Legal Arizona Workers Act (LAWA) on the proportion of the state's population characterized as noncitizen Hispanic. We use the synthetic control method to select a group of states against which Arizona's population trends can be compared. We document a notable and statistically significant reduction in the proportion of the Hispanic noncitizen population in Arizona. The decline observed matches the timing of LAWA's implementation, deviates from the time series for the synthetic control group, and stands out relative to the distribution of placebo estimates for other states in the nation.
Social Networks and Research Output
Authors: Ductor Lorenzo , Fafchamps Marcel , Goyal Sanjeev , van der Leij Marco J. 
Published: November 2013

Abstract
We study how knowledge about the social network of an individual researcher, as embodied in his coauthor relations, helps us in developing a more accurate prediction of his or her future productivity. We find that incorporating information about coauthor networks leads to a modest improvement in the accuracy of forecasts on individual output, over and above what we can predict based on the knowledge of past individual output. Second, we find that the informativeness of networks dissipates over the lifetime of a researcher's career. This suggests that the signaling content of the network is quantitatively more important than the flow of ideas.
Variability of Southern Ocean Jets near Topography
Authors: Chapman Christopher C. , Morrow Rosemary 
Published: November 2013

Abstract
The interaction of jets with topography in the Southern Ocean is investigated using 19 years of altimetry data. In particular, the “jet jumping” mode of variability, by which two or more jets passing close to the same topographic feature show strongly anticorrelated strengthening and weakening, is studied. Three regional case studies are described—the Southeast Indian Ridge south of Tasmania, the Macquarie Ridge south of New Zealand, and the Pacific–Antarctic Rise—where the jet jumping variability is found to occur. Using principal component analysis, the spatial patterns of variability show a vortex dipole forming on either side of a particular jet. For each regional study, it is found that the variability in strength of these vortices (as measured by the spatially averaged vorticity) is strongly correlated with time series of the principle component that describes the jet jumping variability. The observational analysis is complemented by a suite of idealized numerical experiments using a three-layer quasigeostrophic model with simple topography. The numerical results show similar spatial patterns of variability to those observed in the altimetric data. Internal variability is sufficient to generate jet jumping variability, as there is no time-varying external forcing applied in the model configuration. The simulations are used to investigate the effect of topographic scale and changing bottom friction. The authors find that both have a strong influence on the time scale of the variability, with larger topographic scales and higher bottom friction leading to faster time scales. This study shows that even in regions where the flow is strongly influenced by topography, Southern Ocean jet flow may exhibit low-frequency variability.
LysoTracker is a marker of differentiated alveolar type II cells
Authors: Van der Velden Joanne L , Bertoncello Ivan , McQualter Jonathan L 
Published: November 2013

Abstract

Background
LysoTracker Green DND-26 is a fluorescent dye that stains acidic compartments in live cells and has been shown to selectively accumulate in lamellar bodies in alveolar type II (AT2) cells in the lung. The aim of this study was to determine whether the accumulation of LysoTracker in lamellar bodies can be used to isolate viable AT2 cells by flow cytometry and track their differentiation in live-cell culture by microscopy.

Methods
Mouse lung cells were sorted on the basis of CD45negCD31negEpCAMposLysoTrackerpos expression and characterized by immunostaining for SP-C and cultured in a three-dimensional epithelial colony-forming unit (CFU-Epi) assay. To track AT2 cell differentiation, lung epithelial stem and progenitor cells were cultured in a CFU-Epi assay with LysoTracker-supplemented media.

Results
The purity of sorted AT2 cells as determined by SP-C staining was 97.4% and viability was 85.3%. LysoTrackerpos AT2 cells generated SP-Cpos alveolar epithelial cell colonies in culture, and when added to the CFU-Epi culture medium, LysoTracker marked the differentiation of stem/progenitor-derived AT2 cells.

Conclusions
This study describes a novel method for isolating AT2 cells from mouse lungs. The high purity and viability of cells attained by this method, makes them suitable for functional analysis in vitro. The application of LysoTracker to live cell cultures will allow better assessment of the cellular and molecular mechanisms that regulate AT2 cell differentiation.
High presence/absence gene variability in defense-related gene clusters of Cucumis melo
Authors: González Víctor M , Aventín Núria , Centeno Emilio , Puigdomènech Pere 
Published: November 2013

Abstract

Background
Changes in the copy number of DNA sequences are one of the main mechanisms generating genome variability in eukaryotes. These changes are often related to phenotypic effects such as genetic disorders or novel pathogen resistance. The increasing availability of genome sequences through the application of next-generation massive sequencing technologies has allowed the study of genomic polymorphisms at both the interspecific and intraspecific levels, thus helping to understand how species adapt to changing environments through genome variability.

Results
Data on gene presence/absence variation (PAV) in melon was obtained by resequencing a cultivated accession and an old-relative melon variety, and using previously obtained resequencing data from three other melon cultivars, among them DHL92, on which the current draft melon genome sequence is based. A total of 1,697 PAV events were detected, involving 4.4% of the predicted melon gene complement. In all, an average 1.5% of genes were absent from each analyzed cultivar as compared to the DHL92 reference genome. The most populated functional category among the 304 PAV genes of known function was that of stress response proteins (30% of all classified PAVs). Our results suggest that genes from multi-copy families are five times more likely to be affected by PAV than singleton genes. Also, the chance of genes present in the genome in tandem arrays being affected by PAV is double that of isolated genes, with PAV genes tending to be in longer clusters. The highest concentration of PAV events detected in the melon genome was found in a 1.1 Mb region of linkage group V, which also shows the highest density of melon stress-response genes. In particular, this region contains the longest continuous gene-containing PAV sequence so far identified in melon.

Conclusions
The first genome-wide report of PAV variation among several melon cultivars is presented here. Multi-copy and clustered genes, especially those with putative stress-response functions, were found to be particularly affected by PAV polymorphisms. As cucurbits are known to possess a significantly lower number of defense-related genes compared to other plant species, PAV variation may play an important role in generating new pathogen resistances at the subspecies level. In addition, these results show the limitations of single reference genome sequences as the only basis for characterization and cloning of resistance genes.