bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physical properties and biocompatibility of UHMWPE-derived materials modified by synchrotron radiation
Authors: Bykova Iu. , Weinhardt V. , Kashkarova A. , Lebedev S. , Baumbach T. , Pichugin V. , Zaitsev K. , Khlusov I. 
Published: May 2014

Abstract
The applications of synchrotron radiation (SR) in medical imaging have become of great use, particularly in angiography, bronchography, mammography, computed tomography, and X-ray microscopy. Thanks to recently developed phase contrast imaging techniques non-destructive preclinical testing of low absorbing materials such as polymers has become possible. The focus of the present work is characterization and examination of UHMWPE-derived materials widely used in medicine, before and after their exposure to SR during such testing. Physical properties, such as wettability, surface energy, IR-spectroscopy, roughness, optical microscopy, microhardness measurements of UHMWPE samples were studied before and after SR. The relationship between a growth of UHMWPE surface hydrophilicity after SR and surface colonization by stromal cells was studied in vitro. Obtained results demonstrate that SR may be used as prospective direction to examine bulk (porous) structure of polymer materials and/or to modify polymer surface and volume for tissue engineering.
Cost Sharing and Hereditary Cancer Risk: Predictors of Willingness‐to‐Pay for Genetic Testing
Authors: Matro Jennifer M. , Ruth Karen J. , Wong Yu‐Ning , McCully Katen C. , Rybak Christina M. , Meropol Neal J. , Hall Michael J. 
Published: May 2014

AbstractIncreasing use of predictive genetic testing to gauge hereditary cancer risk has been paralleled by rising cost‐sharing practices. Little is known about how demographic and psychosocial factors may influence individuals’ willingness‐to‐pay for genetic testing. The Gastrointestinal Tumor Risk Assessment Program Registry includes individuals presenting for genetic risk assessment based on personal/family cancer history. Participants complete a baseline survey assessing cancer history and psychosocial items. Willingness‐to‐pay items include intention for: genetic testing only if paid by insurance; testing with self‐pay; and amount willing‐to‐pay ($25–$2,000). Multivariable models examined predictors of willingness‐to‐pay out‐of‐pocket (versus only if paid by insurance) and willingness‐to‐pay a smaller versus larger sum (≤$200 vs. ≥$500). All statistical tests are two‐sided (α = 0.05). Of 385 evaluable participants, a minority (42 %) had a personal cancer history, while 56 % had ≥1 first‐degree relative with colorectal cancer. Overall, 21.3 % were willing to have testing only if paid by insurance, and 78.7 % were willing‐to‐pay. Predictors of willingness‐to‐pay were: 1) concern for positive result; 2) confidence to control cancer risk; 3) fewer perceived barriers to colorectal cancer screening; 4) benefit of testing to guide screening (all p < 0.05). Subjects willing‐to‐pay a higher amount were male, more educated, had greater cancer worry, fewer relatives with colorectal cancer, and more positive attitudes toward genetic testing (all p < 0.05). Individuals seeking risk assessment are willing‐to‐pay out‐of‐pocket for genetic testing, and anticipate benefits to reducing cancer risk. Identifying factors associated with willingness‐to‐pay for genetic services is increasingly important as testing is integrated into routine cancer care.
Subtype‐dependent prognostic relevance of an interferon‐induced pathway metagene in node‐negative breast cancer
Authors: Callari Maurizio , Musella Valeria , Di Buduo Eleonora , Sensi Marialuisa , Miodini Patrizia , Dugo Matteo , Orlandi Rosaria , Agresti Roberto , Paolini Biagio , Carcangiu Maria Luisa , Cappelletti Vera , Daidone Maria Grazia 
Published: May 2014

The majority of gene expression signatures developed to predict the likelihood to relapse in breast cancer (BC) patients assigns a high risk score to patients with Estrogen Receptor (ER) negative or highly proliferating tumors. We aimed to identify a signature of differentially expressed (DE) metagenes, rather than single DE genes, associated with distant metastases beyond classical risk factors.We used 105 gene expression profiles from consecutive BCs to identify metagenes whose prognostic role was defined on an independent series of 92 ESR1+/ERBB2− node‐negative BCs (42 cases developing metastases within 5 years from diagnosis and 50 cases metastasis‐free for more than 5 years, comparable for age, tumor size, ER status and surgery). Findings were validated on publicly available datasets of 684 node‐negative BCs including all the subtypes.Only a metagene containing interferon‐induced genes (IFN metagene) proved to be predictive of distant metastasis in our series of patients with ESR1+/ERBB2− tumors (P = 0.029), and such a finding was validated on 457 ESR1+/ERBB2− BCs from public datasets (P = 0.0424). Conversely, the IFN metagene was associated with a low risk of metastasis in 104 ERBB2+ tumors (P = 0.0099) whereas it did not prove to significantly affect prognosis in 123 ESR1−/ERBB2− tumors (P = 0.2235). A complex prognostic interaction was revealed in ESR1+/ERBB2− and ERBB2+ tumors when the association between the IFN metagene and a T‐cell metagene was considered.The study confirms the importance of analyzing prognostic variables separately within BC subtypes, highlights the advantages of using metagenes rather than genes, and finally identifies in node‐negative ESR1+/ERBB2− BCs, the unfavorable role of high IFN metagene expression.
The political economy of foreign direct investment—Evidence from the Philippines
Authors: Drope Jeffrey , Chavez Jenina Joy , Lencucha Raphael , McGrady Benn 
Published: May 2014

AbstractMuch of the conventional wisdom about the political economy of foreign direct investment suggests that many developing country governments lower regulatory and/or legislative standards in order to woo potential investors. Using the case of the tobacco industry's efforts to influence excise tax policy reforms in the Philippines, we find a much more complex reality. Over a period of more than 15 years of concerted efforts and significant financial investment, a large multinational tobacco firm was consistently unable to realize its tax policy goals with serious, negative implications for the firm. In the most recent major policy confrontation over excise tax reform that led to one of the largest tax increases on tobacco products ever in a developing country, a number of major variables mitigated the powerful firm's influence. These variables included strong support for tax reform from a number of influential political actors and a well-organized civil society movement, which led to broader public support for both public health and fiscal reasons. Global governance around economic policy and the effects of domestic institutional structures also had marked effects on the outcomes.
MEDICAL DEVICES EARLY ASSESSMENT METHODS: SYSTEMATIC LITERATURE REVIEW
Authors: Markiewicz Katarzyna , van Til Janine A. , IJzerman Maarten J. 
Published: May 2014

Objectives:The aim of this study was to get an overview of current theory and practice in early assessments of medical devices, and to identify aims and uses of early assessment methods used in practice.Methods:A systematic literature review was conducted in September 2013, using computerized databases (PubMed, Science Direct, and Scopus), and references list search. Selected articles were categorized based on their type, objective, and main target audience. The methods used in the application studies were extracted and mapped throughout the early stages of development and for their particular aims.Results:Of 1,961 articles identified, eighty-three studies passed the inclusion criteria, and thirty were included by searching reference lists. There were thirty-one theoretical papers, and eighty-two application papers included. Most studies investigated potential applications/possible improvement of medical devices, developed early assessment framework or included stakeholder perspective in early development stages. Among multiple qualitative and quantitative methods identified, only few were used more than once. The methods aim to inform strategic considerations (e.g., literature review), economic evaluation (e.g., cost-effectiveness analysis), and clinical effectiveness (e.g., clinical trials). Medical devices were often in the prototype product development stage, and the results were usually aimed at informing manufacturers.Conclusions:This study showed converging aims yet widely diverging methods for early assessment during medical device development. For early assessment to become an integral part of activities in the development of medical devices, methods need to be clarified and standardized, and the aims and value of assessment itself must be demonstrated to the main stakeholders for assuring effective and efficient medical device development.
Characterizing fundamental parameter-based analysis for soil–ceramic matrices in polarized energy-dispersive X-ray fluorescence (PEDXRF) spectrometry
Authors: Abuhani Waleed Amin , Dasgupta-Schubert Nabanita , Villaseñor Cendejas Luis Manuel 
Published: May 2014

Analytical polarized energy-dispersive X-ray fluorescence (PEDXRF) spectrometry (PEDXRFS) represents a substantial advancement over conventional XRF. The higher signal-to-noise commensurate with background lowering and better energy resolution, permits trace analysis for elements with Z ≥ 11. Concomitantly, improvements in analytical software based on the fundamental parameters (FP) approach have improved accuracies and precisions for standard-less analysis (SLA). Two ceramic and soil standard reference materials (SRMs), 98a-Plastic Clay and GSS-1 powders, differed in their intrinsic matrix properties of grain size, bulk, and surface monolayer densities as well as the elemental concentrations. The SRMs were analyzed as powder and as pellets compacted under the same pressure conditions to double the bulk density. Different geometries represented by the sample cup (10, 15, and 24 mm) and pellet (10, 15, and 25 mm) diameters with the same sample thickness (with differing masses and aspect ratios), as well as (for powder samples only) identical low masses (0.5 g) but with varying thicknesses, were analyzed. PEDXRFS combined with TURBOQUANT® (TQ) as SLA-FP enables good quantitative analysis for powders (Z ≥ 13) even for masses significantly lower than recommended, for soil–ceramic samples. Pellets (Z ≥ 12) yielded the best accuracy factor (AF) at high aspect ratio and thicknesses of the matrix analytical depth. Binder in pellets depreciates the AF. TQ needs to adequately quantitate matrix interferences effects, to improve accuracy in the analysis of low atomic numbers, e.g. Na and Mg.
An order parameter for impurity systems at quantum criticality
Authors: Bayat Abolfazl , Johannesson Henrik , Bose Sougato , Sodano Pasquale 
Published: May 2014

AbstractA quantum phase transition may occur in the ground state of a system at zero temperature when a controlling field or interaction is varied. The resulting quantum fluctuations which trigger the transition produce scaling behaviour of various observables, governed by universal critical exponents. A particularly interesting class of such transitions appear in systems with quantum impurities where a non-extensive term in the free energy becomes singular at the critical point. Curiously, the notion of a conventional order parameter that exhibits scaling at the critical point is generically missing in these systems. Here we explore the possibility to use the Schmidt gap, which is an observable obtained from the entanglement spectrum, as an order parameter. A case study of the two-impurity Kondo model confirms that the Schmidt gap faithfully captures the scaling behaviour by correctly predicting the critical exponent of the dynamically generated length scale at the critical point.
Encouraging Reductions in Nonpoint Source Pollution through Point‐nonpoint Trading: The Roles of Baseline Choice and Practice Subsidies
Authors: Ribaudo Marc , Savage Jeffrey , Talberth John 
Published: May 2014

AbstractWater quality regulations in the United States apply almost exclusively to point sources. In impaired watersheds where both point and nonpoint sources contribute to pollution, the U.S. Environmental Protection Agency (EPA) is encouraging the use of point‐nonpoint trading to reduce the cost of point sources to meet their permit requirement, and to encourage nonpoint sources to voluntarily contribute more towards meeting overall water quality goals. The EPA guidance encourages trading programs to set a nonpoint source eligibility baseline that extracts some “extra” abatement from nonpoint sources. Research has shown that setting an eligibility baseline that is substantially more stringent than current management could discourage nonpoint source participation and significantly hinder trading. In this paper we examine how choosing the eligibility baseline for agricultural sources affects the efficiency goal of trading (reducing costs to point sources), as well as how it affects the EPA goal of encouraging nonpoint abatement. Using data from the Chesapeake Bay Watershed we find that eligibility baselines set to encourage additional nonpoint source abatement reduce the supply of credits in a market; the more stringent the baseline, the fewer the trades and the smaller the overall abatement from nonpoint sources. A subsidy to farmers for reducing the cost of meeting a baseline encourages greater nonpoint source abatement, but may not benefit the trading market.
The Effects of Agricultural Technological Progress on Deforestation: What Do We Really Know?
Authors: Villoria Nelson B. , Byerlee Derek , Stevenson James 
Published: May 2014

AbstractIncreasing agricultural yields seem an obvious way to satisfy increasing demands for food and fuel while minimizing expansion of agriculture into forest areas; however, an influential literature worries that promoting agricultural innovation could enhance agriculture's profitability thereby encouraging deforestation. Clarifying the effects of agricultural technological progress on deforestation is therefore crucial for designing effective policy responses to the challenges faced by global agriculture. In this article we review the empirical evidence on these effects and synthesize estimates of future global cropland expansion. Our main insights are that: (i) the empirical evidence on a positive link between regional technological progress and deforestation is much weaker than what seems generally accepted; (ii) at a global level, most analysts expect broad based technological progress to be land saving; however, composition effects are important as low‐yield, land‐abundant regions are likely to experience further land expansion. Toward the future, empirical work understanding how localized technological progress in agriculture transmits through international trade and commodity markets will help to bridge the gap between the findings of local, econometric, studies on the one hand and global, model based, studies on the other.
Estimating the Impact of Education on Household Fruit and Vegetable Purchases
Authors: Berning Joshua , Hogan John J. 
Published: May 2014

AbstractWe examine the effect that investments in education have on household expenditure on fruits and vegetables using a two‐stage model that accounts for differences in ability and heterogeneous returns to education. For this, we use the 2008 Consumer Expenditure Survey for the United States. We find that higher levels of education contribute to greater household expenditures on both fresh and processed fruits and vegetables. We find a nonlinear effect on fresh fruits and vegetables, indicating that education impacts the quality of purchases as well. Although nutritional education is often touted as important for a healthful diet, these results highlight how investments in human capital via formal education can potentially improve dietary quality as well.
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
Authors: Choi Meena , Chang Ching-Yun , Clough Timothy , Broudy Daniel , Killeen Trevor , MacLean Brendan , Vitek Olga 
Published: May 2014

Summary: MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models.
Availability and implementation: The code, the documentation and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org and used in an R command line workflow. The package can also be accessed as an external tool in Skyline (Broudy et al., 2014) and used via graphical user interface.
Contact: ovitek@purdue.edu
Mirin: identifying microRNA regulatory modules in protein–protein interaction networks
Authors: Yang Ken-Chi , Hsu Chia-Lang , Lin Chen-Ching , Juan Hsueh-Fen , Huang Hsuan-Cheng 
Published: May 2014

Summary: Exploring microRNA (miRNA) regulations and protein–protein interactions could reveal the molecular mechanisms responsible for complex biological processes. Mirin is a web-based application suitable for identifying functional modules from protein–protein interaction networks regulated by aberrant miRNAs under user-defined biological conditions such as cancers. The analysis involves combining miRNA regulations, protein–protein interactions between target genes, as well as mRNA and miRNA expression profiles provided by users. Mirin has successfully uncovered oncomirs and their regulatory networks in various cancers, such as gastric and breast cancer.
Availability and implementation: Mirin is freely available at http://mirin.ym.edu.tw/.
Contact: hsuancheng@ym.edu.tw or yukijuan@ntu.edu.tw
Supplementary information: Supplementary Data are available at Bioinformatics online.
A comparison of algorithms for the pairwise alignment of biological networks
Authors: Clark Connor , Kalita Jugal 
Published: May 2014

Motivation: As biological inquiry produces ever more network data, such as protein–protein interaction networks, gene regulatory networks and metabolic networks, many algorithms have been proposed for the purpose of pairwise network alignment—finding a mapping from the nodes of one network to the nodes of another in such a way that the mapped nodes can be considered to correspond with respect to both their place in the network topology and their biological attributes. This technique is helpful in identifying previously undiscovered homologies between proteins of different species and revealing functionally similar subnetworks. In the past few years, a wealth of different aligners has been published, but few of them have been compared with one another, and no comprehensive review of these algorithms has yet appeared.
Results: We present the problem of biological network alignment, provide a guide to existing alignment algorithms and comprehensively benchmark existing algorithms on both synthetic and real-world biological data, finding dramatic differences between existing algorithms in the quality of the alignments they produce. Additionally, we find that many of these tools are inconvenient to use in practice, and there remains a need for easy-to-use cross-platform tools for performing network alignment.
Contact: cclark@uccs.edu, jkalita@uccs.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity
Authors: Nedumpully-Govindan Praveen , Li Lin , Alexov Emil G. , Blenner Mark A. , Ding Feng 
Published: May 2014

Motivation: Tyrosine sulfation is a type of post-translational modification (PTM) catalyzed by tyrosylprotein sulfotransferases (TPST). The modification plays a crucial role in mediating protein–protein interactions in many biologically important processes. There is no well-defined sequence motif for TPST sulfation, and the underlying determinants of TPST sulfation specificity remains elusive. Here, we perform molecular modeling to uncover the structural and energetic determinants of TPST sulfation specificity.
Results: We estimate the binding affinities between TPST and peptides around tyrosines of both sulfated and non-sulfated proteins to differentiate them. We find that better differentiation is achieved after including energy costs associated with local unfolding of the tyrosine-containing peptide in a host protein, which depends on both the peptide’s secondary structures and solvent accessibility. Local unfolding renders buried peptide—with ordered structures—thermodynamically available for TPST binding. Our results suggest that both thermodynamic availability of the peptide and its binding affinity to the enzyme are important for TPST sulfation specificity, and their interplay results into great variations in sequences and structures of sulfated peptides. We expect our method to be useful in predicting potential sulfation sites and transferable to other TPST variants. Our study may also shed light on other PTM systems without well-defined sequence and structural specificities.
Availability and implementation: All the data and scripts used in the work are available at http://dlab.clemson.edu/research/Sulfation.
Contact: fding@clemson.edu
Supplementary information: Supplementary Data are available at Bioinformatics online.
Bioclojure: a functional library for the manipulation of biological sequences
Authors: Plieskatt Jordan , Rinaldi Gabriel , Brindley Paul J. , Jia Xinying , Potriquet Jeremy , Bethony Jeffrey , Mulvenna Jason 
Published: May 2014

Motivation: BioClojure is an open-source library for the manipulation of biological sequence data written in the language Clojure. BioClojure aims to provide a functional framework for the processing of biological sequence data that provides simple mechanisms for concurrency and lazy evaluation of large datasets.
Results: BioClojure provides parsers and accessors for a range of biological sequence formats, including UniProtXML, Genbank XML, FASTA and FASTQ. In addition, it provides wrappers for key analysis programs, including BLAST, SignalP, TMHMM and InterProScan, and parsers for analyzing their output. All interfaces leverage Clojure’s functional style and emphasize laziness and composability, so that BioClojure, and user-defined, functions can be chained into simple pipelines that are thread-safe and seamlessly integrate lazy evaluation.
Availability and implementation: BioClojure is distributed under the Lesser GPL, and the source code is freely available from GitHub (https://github.com/s312569/clj-biosequence).
Contact: jason.mulvenna@qimrberghofer.edu.au or jason.mulvenna@qimr.edu.au
unifiedWMWqPCR: the unified Wilcoxon–Mann–Whitney test for analyzing RT-qPCR data in R
Authors: De Neve Jan , Meys Joris , Ottoy Jean–Pierre , Clement Lieven , Thas Olivier 
Published: May 2014

Motivation: Recently, De Neve et al. proposed a modification of the Wilcoxon–Mann–Whitney (WMW) test for assessing differential expression based on RT-qPCR data. Their test, referred to as the unified WMW (uWMW) test, incorporates a robust and intuitive normalization and quantifies the probability that the expression from one treatment group exceeds the expression from another treatment group. However, no software package for this test was available yet.
Results: We have developed a Bioconductor package for analyzing RT-qPCR data with the uWMW test. The package also provides graphical tools for visualizing the effect sizes.
Availability and implementation: The unifiedWMWqPCR package and its user documentation can be obtained through Bioconductor.
Contact: JanR.DeNeve@UGent.be