bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ice sheets as a significant source of highly reactive nanoparticulate iron to the oceans
Authors: Hawkings Jon R. , Wadham Jemma L. , Tranter Martyn , Raiswell Rob , Benning Liane G. , Statham Peter J. , Tedstone Andrew , Nienow Peter , Lee Katherine , Telling Jon 
Published: May 2014

AbstractThe Greenland and Antarctic Ice Sheets cover ~\n10% of global land surface, but are rarely considered as active components of the global iron cycle. The ocean waters around both ice sheets harbour highly productive coastal ecosystems, many of which are iron limited. Measurements of iron concentrations in subglacial runoff from a large Greenland Ice Sheet catchment reveal the potential for globally significant export of labile iron fractions to the near-coastal euphotic zone. We estimate that the flux of bioavailable iron associated with glacial runoff is 0.40–2.54 Tg per year in Greenland and 0.06–0.17 Tg per year in Antarctica. Iron fluxes are dominated by a highly reactive and potentially bioavailable nanoparticulate suspended sediment fraction, similar to that identified in Antarctic icebergs. Estimates of labile iron fluxes in meltwater are comparable with aeolian dust fluxes to the oceans surrounding Greenland and Antarctica, and are similarly expected to increase in a warming climate with enhanced melting.
Powerful inner/outer controlled multi-target magnetic nanoparticle drug carrier prepared by liquid photo-immobilization
Authors: Guan Yan-Qing , Zheng Zhe , Huang Zheng , Li Zhibin , Niu Shuiqin , Liu Jun-Ming 
Published: May 2014

AbstractNanomagnetic materials offer exciting avenues for advancing cancer therapies. Most researches have focused on efficient delivery of drugs in the body by incorporating various drug molecules onto the surface of nanomagnetic particles. The challenge is how to synthesize low toxic nanocarriers with multi-target drug loading. The cancer cell death mechanisms associated with those nanocarriers remain unclear either. Following the cell biology mechanisms, we develop a liquid photo-immobilization approach to attach doxorubicin, folic acid, tumor necrosis factor-α and interferon-γ onto the oleic acid molecules coated Fe3O4 magnetic nanoparticles to prepare a kind of novel inner/outer controlled multi-target magnetic nanoparticle drug carrier. In this work, this approach is demonstrated by a variety of structural and biomedical characterizations, addressing the anti-cancer effects in vivo and in vitro on the HeLa and it is highly efficient and powerful in treating cancer cells in a valuable programmed cell death mechanism for overcoming drug resistance.
Chromatin fiber polymorphism triggered by variations of DNA linker lengths
Authors: Collepardo-Guevara Rosana , Schlick Tamar 
Published: May 2014

Significance
The structure of the chromatin fiber remains one of the most fundamental open biological questions because structure dictates many template-directed processes. We use coarse-grained modeling to investigate systematically how variations in the linker DNA length that arise naturally for chromatin in different tissues, species, and cell cycle stages affect fiber architecture. We unravel a natural source of fiber polymorphism, in which irregular interdigitated 10-nm and compact 30-nm fibers coexist. These results suggest how structural diversity can be advantageous for gene regulation activity. Interesting DNA design applications also arise.
OPG/RANKL/RANK axis is a critical inflammatory signaling system in ischemic brain in mice
Authors: Shimamura Munehisa , Nakagami Hironori , Osako Mariana K. , Kurinami Hitomi , Koriyama Hiroshi , Zhengda Pang , Tomioka Hideki , Tenma Akiko , Wakayama Kouji , Morishita Ryuichi 
Published: May 2014

SignificanceAlthough a high-serum osteoprotegerin (OPG) level is associated with an unfavorable outcome in ischemic stroke, it is unclear whether OPG is a culprit or an innocent bystander. Here we show that the deletion of OPG and enhanced RANKL/RANK signaling contribute to the reduction of infarct volume with lower brain edema, whereas infarct volume is increased by reduced RANKL/RANK signaling inOPG−/−mice and WT mice treated with anti-RANKL neutralizing antibody. OPG, RANKL, and RANK mRNA were increased in ischemic brain and were expressed in activated microglia and macrophages. Enhanced RANKL/RANK signaling showed neuroprotective effects with reduced expression in inflammatory cytokines in LPS-stimulated neuron-glia mixed culture. Our findings propose anti-inflammatory roles for RANKL/RANK signaling in ischemic brains.
Exploration and retrieval of whole-metagenome sequencing samples
Authors: Seth Sohan , Välimäki Niko , Kaski Samuel , Honkela Antti 
Published: May 2014

Motivation: Over the recent years, the field of whole-metagenome shotgun sequencing has witnessed significant growth owing to the high-throughput sequencing technologies that allow sequencing genomic samples cheaper, faster and with better coverage than before. This technical advancement has initiated the trend of sequencing multiple samples in different conditions or environments to explore the similarities and dissimilarities of the microbial communities. Examples include the human microbiome project and various studies of the human intestinal tract. With the availability of ever larger databases of such measurements, finding samples similar to a given query sample is becoming a central operation.
Results: In this article, we develop a content-based exploration and retrieval method for whole-metagenome sequencing samples. We apply a distributed string mining framework to efficiently extract all informative sequence k-mers from a pool of metagenomic samples and use them to measure the dissimilarity between two samples. We evaluate the performance of the proposed approach on two human gut metagenome datasets as well as human microbiome project metagenomic samples. We observe significant enrichment for diseased gut samples in results of queries with another diseased sample and high accuracy in discriminating between different body sites even though the method is unsupervised.
Availability and implementation: A software implementation of the DSM framework is available at https://github.com/HIITMetagenomics/dsm-framework.
Contact: sohan.seth@hiit.fi or antti.honkela@hiit.fi
Supplementary information: Supplementary Data are available at Bioinformatics online.
Estimates of allele-specific expression in
Drosophila
with a single genome sequence and RNA-seq data
Authors: Quinn Andrew , Juneja Punita , Jiggins Francis M. 
Published: May 2014

Abstract
Motivation: Genetic variation in cis -regulatory elements is an important cause of variation in gene expression. Cis -regulatory variation can be detected by using high-throughput RNA sequencing (RNA-seq) to identify differences in the expression of the two alleles of a gene. This requires that reads from the two alleles are equally likely to map to a reference genome(s), and that single-nucleotide polymorphisms (SNPs) are accurately called, so that reads derived from the different alleles can be identified. Both of these prerequisites can be achieved by sequencing the genomes of the parents of the individual being studied, but this is often prohibitively costly.
Results: In Drosophila , we demonstrate that biases during read mapping can be avoided by mapping reads to two alternative genomes that incorporate SNPs called from the RNA-seq data. The SNPs can be reliably called from the RNA-seq data itself, provided any variants not found in high-quality SNP databases are filtered out. Finally, we suggest a way of measuring allele-specific expression (ASE) by crossing the line of interest to a reference line with a high-quality genome sequence. Combined with our bioinformatic methods, this approach minimizes mapping biases, allows poor-quality data to be identified and removed and aides in the biological interpretation of the data as the parent of origin of each allele is known. In conclusion, our results suggest that accurate estimates of ASE do not require the parental genomes of the individual being studied to be sequenced.
Availability and implementation: Scripts used to perform our analysis are available at https://github.com/d-quinn/bio_quinn2013 .
Contact: fmj1001@cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Low Bone Mineral Mass Is Associated With Decreased Bone Formation and Diet in Girls With Rett Syndrome
Authors: Motil Kathleen J. , Barrish Judy O. , Neul Jeffrey L. , Glaze Daniel G. 
Published: May 2014

ABSTRACTObjective:The aim of the present study was to characterize biomarkers of bone turnover and their relation with bone mineral mass in a cross‐sectional cohort of girls with Rett syndrome (RTT) and to examine the role of dietary, biochemical, hormonal, and inflammatory factors on bone mineral mass and bone biomarkers in this disorder.Methods:Total body bone mineral content (BMC) and bone mineral density (BMD) were determined by dual‐energy x‐ray absorptiometry. Dietary nutrient intakes were determined from 3‐day food records. Biomarkers of bone turnover, bone metabolites, vitamin D metabolites, hormones, and inflammatory markers were measured by standard clinical laboratory methods.Results:Serum osteocalcin, bone alkaline phosphatase, and C‐telopeptide showed significant inverse relations with age in the RTT cohort. Mean osteocalcin concentrations were significantly lower and mean bone alkaline phosphatase concentrations were significantly higher for individual age groups in the RTT cohort than mean values for their respective age ranges in the reference population. Significant inverse associations were identified between urinary calcium losses, expressed as calcium:creatinine ratios, and total body BMC and BMD z scores. Dietary protein, calcium, and phosphorus intakes, expressed as a proportion of Dietary Reference Intakes for age and sex, showed significant positive associations with total body BMD z scores.Conclusions:The present study suggests decreased bone formation instead of increased bone resorption may explain in part the deficits in bone mineral mass in RTT and that attention to the adequacy of dietary protein, calcium, and phosphorus intakes may offer an opportunity to improve bone health in RTT.
The Liver in Pediatric Gastrointestinal Disease
Authors: Vo Hanh D. , Xu Jiliu , Rabinowitz Simon S. , Fisher Stanley E. , Schwarz Steven M. 
Published: May 2014

ABSTRACTHepatic involvement is often encountered in gastrointestinal (GI) diseases, in part because of the close anatomic and physiologic relations between the liver and GI tract. Drainage of the mesenteric blood supply to the portal vein permits absorbed and/or translocated nutrients, toxins, bacterial elements, cytokines, and immunocytes to gain hepatic access. Liver problems in digestive disorders may range from nonspecific hepatocellular enzyme elevations to significant pathologic processes that may progress to end‐stage liver disease. Hepatobiliary manifestations of primary GI diseases in childhood and adolescence are not uncommon and include several well‐described associations, such as sclerosing cholangitis with inflammatory bowel disease. Liver damage may also result from the effects of drugs used to treat GI diseases, for example, the hepatotoxicity of immunomodulatory therapies. This review highlights the important features of the hepatic and biliary abnormalities associated with 3 common pediatric GI conditions: inflammatory bowel disease, celiac disease, and cystic fibrosis.
Consumer willingness to pay for organic fresh milk in Taiwan
Authors: Huang Chin-Huang , Lee Chun-Hung 
Published: May 2014

Purpose
– The Fresh Milk Logo certifies that dairy product sold in Taiwan really is fresh milk. However, the logo represents only a moral pledge by the manufacturer. No method exists for inspecting whether products are fresh milk or reconstituted milk, and the label does not represent a commitment to the same level of quality and consumer health protection as found in organic foods. The purpose of this paper is to analyze consumer perceptions of organic certified agricultural standards (CAS) and estimates consumer willingness to pay (WTP) a premium should the Fresh Milk Logo be transformed into an organic CAS certified label.

Design/methodology/approach
– Exploratory factor analysis is adopted to extract the main determinants of respondent perceptions and preferences. Additionally, the double-bounded dichotomous choice of the contingent valuation method (CVM) and survival function is used to measure consumer WTP a premium for organic fresh milk.

Findings
– Consumer consumption preferences for buying fresh milk extracted four main factorial dimensions: Fresh Milk Logo, price/promotion, organic, and product/brand. Respondents are willing to pay US$21.95 extra per year to buy organic CAS milk and the factors affecting WTP are “Fresh Milk Logo” and “organic”.

Research limitations/implications
– The problems of the CVM include hypothetical and starting point for price bidding. The double-bounded dichotomous choice contingent valuation model and pre-testing can reduce the biases. The survival function is more flexible, yields more information and permits assumptions regarding parametric distributions without additional costs. The collaboration of survival function with the double-bounded method produces a reliable result that incorporates fewer statistical errors.

Practical implications
– Consumers are willing to pay a premium for fresh milk with an organic CAS label that certifies its good quality and safety.

Social implications
– Marketing managers can use the study findings to develop effective marketing strategies and refine advertising campaigns to promote organic fresh milk to attract more consumers.

Originality/value
– Organic food labels certify food safety, and are associated with the trend toward increasing awareness of environmental and health issues. Perception of organic food labels are introduced into double-bounded dichotomous choice CVM to estimate consumers’ WTP, an approach which has successfully dominated traditional methods, using Likert scale-type measurement.
Food safety incidents’ influence on the food industry
Authors: Zeng Kaisheng , Luo Xiaohui , Liu Yinglin 
Published: May 2014

Purpose– The purposes of this paper are to find out the correlations between the changes of food companies’ environments and the strategic reactions of food companies after the media disclosed that there were food safety incidents out there in the food markets.Design/methodology/approach– This paper uses a randomly sampling survey of 139 food enterprises in China. After statistical significance and statistical power were examined, canonical correlation analysis was used as the main data analysis technique of this research.Findings– Based on the environment-strategy paradigm, the authors found that the changes of the competition environment, resource environment, and institution environment in the food industry have significant association with food companies’ strategic reactions such as public relations, networking with firms and futurity after food safety incidents in the food market were disclosed.Originality/value– The paper is the first to quantitatively examine the relationships between the changes of food companies’ environments and the strategic reactions of food companies after the media disclosed that there were food safety incidents in the food markets. The findings of this paper send novel and important messages to government decision makers and the public, evidencing how food companies strategically respond to external environmental changes, and suggesting that the institution-builder as well as the media have more work to do in the aftermath of food safety incidents.
Current spectrum estimation using Prony's estimator and coherent resampling
Authors: Lewandowski Michał , Walczak Janusz 
Published: May 2014

Purpose
– A highly accurate method of current spectrum estimation of a nonlinear load is presented in this paper. Using the method makes it possible to evaluate the current injection frequency domain model of a nonlinear load from previously recorded time domain voltage and current waveforms. The paper aims to discuss these issues.

Design/methodology/approach
– The method incorporates the idea of coherent resampling (resampling synchronously with the base frequency of the signal) followed by the discrete Fourier transform (DFT) to obtain the frequency spectrum. When DFT is applied to a synchronously resampled signal, the spectrum is free of negative DFT effects (the spectrum leakage, for example). However, to resample the signal correctly it is necessary to know its base frequency with high accuracy. To estimate the base frequency, the first-order Prony's frequency estimator was used.

Findings
– It has been shown that the presented method may lead to superior results in comparison with window interpolated Fourier transform and time-domain quasi-synchronous sampling algorithms.

Research limitations/implications
– The method was designed for steady-state analysis in the frequency domain. The voltage and current waveforms across load terminals should be recorded simultaneously to allow correct voltage/current phase shift estimation.

Practical implications
– The proposed method can be used in case when the frequency domain model of a nonlinear load is desired and the voltage and current waveforms recorded across load terminals are available. The method leads to correct results even when the voltage/current sampling frequency has not been synchronized with the base frequency of the signal. It can be used for off-line frequency model estimation as well as in real-time DSP systems to restore coherent sampling of the analysed signals.

Originality/value
– The method proposed in the paper allows to estimate a nonlinear load frequency domain model from current and voltage waveforms with higher accuracy than other competitive methods, while at the same time its simplicity and computational efficiency is retained.
Topology optimization of rotor poles in a permanent-magnet machine using level set method and continuum design sensitivity analysis
Authors: Putek Piotr , Paplicki Piotr , Pałka Ryszard 
Published: May 2014

Purpose– In this paper, a numerical approach to the topology optimization is proposed to design the permanent magnet excited machines with improved high-speed features. For this purpose the modified multi-level set method (MLSM) was proposed and applied to capture the shape of rotor poles on the fixed mesh using FE analysis. The paper aims to discuss these issues.Design/methodology/approach– This framework is based on theories of topological and shape derivative for the magnetostatic system. During the iterative optimization process, the shape of rotor poles and its evolution is represented by the level sets of a continuous level set function f. The shape optimization of the iron and the magnet rotor poles is provided by the combining continuum design sensitivity analysis with level set method.Findings– To obtain an innovative design of the rotor poles composed of different materials, the modified MLSM is proposed. An essential advantage of the proposed method is its ability to handle a topology change on a fixed mesh by the nucleating a small hole in design domain that leads to more efficient computational scheme then standard level set method.Research limitations/implications– The proposed numerical approach to the topology design of the 3D model of a PM machine is based on the simplified 2D model under assumption that the eddy currents in both the magnet and iron parts are neglected.Originality/value– The novel aspect of the proposed method is the incorporation of the Total Variation regularization in the MLSM, which distribution is additionally modified by the gradient derivative information, in order to stabilize the optimization process and penalize oscillations without smoothing edges.
Multi-physics optimisation of an energy harvester device for automotive application
Authors: Bonisoli Elvio , Di Monaco Francesco , Tornincasa Stefano , Freschi Fabio , Giaccone Luca , Repetto Maurizio 
Published: May 2014

Purpose
– Supplying remote wireless sensors is not an easy task if the site where the device is located is not easily accessible. In order to obtain direct measurements of the road-vehicle interactions, sensors must be placed inside the tyre environment thus a power supply must be available for their working there without any wire connection with the car main power. The paper aims to discuss these issues.

Design/methodology/approach
– An electro-mechanical energy harvester has thus been developed for supplying an automotive wireless sensor of pressure, temperature and acceleration to be placed on the inner line of a tyre. The primary energy source is the vibrations or variable accelerations imposed to the device and induced in the tyre by the wheeling.

Findings
– The harvester has been designed by means of a multi-physics optimisation based on an integrated electromagnetic-mechanical circuit simulator. Thus an automated optimisation of the device with respect to volume constraints, magnets dimensions, induction coils placement and size have been performed to increase the average power extracted from the device at different wheeling speeds.

Originality/value
– The use of the multi-physics environment together with automated optimisation technique has been tested for the first time on the electromagnetic harvester structure.
Framework for the optimization of online computable models
Authors: Delinchant Benoit , Wurtz Frédéric , Vasconcelos João , Coulomb Jean-Louis 
Published: May 2014

Purpose
– The purpose of this paper is to make easily accessible models to test and compare the optimization algorithms we develop.

Design/methodology/approach
– For this, the paper proposes an optimization framework based on software component, web service, and plugin to exploit these models in different environments.

Findings
– The paper illustrates the discussion with optimizations in Matlab™ and R (www.r-project.org) of a transformer described and exploitable from the internet.

Originality/value
– The originality is to make easy implementation of simulation model and optimization algorithm coupling using software component, web service, and plugin.
Use of compensation theorem for the robustness assessment of electromagnetic devices optimal design
Authors: Formisano Alessandro , Fresa Raffaele , Martone Raffaele 
Published: May 2014

Purpose
– The purpose of this paper is to present the use of the compensation theorem (CT), well known in the analysis of linear electric networks, to compute sensitivity of the performance functions used in the robust design or tolerance analysis of electromagnetic devices.

Design/methodology/approach
– The CT is first illustrated in the case of a simple field analysis problem. Then, using numerical simulations, the effectiveness of compensation approach for assessing impact of the small modification of material properties is shown. The numerical simulations are performed with a finite elements code based on an integral formulation.

Findings
– The complexity of additional computations to assess the effect of small variations involved in sensitivity analysis can be reduced.

Research limitations/implications
– The method can be applied only to linear systems; in addition, although compensation applies to any variations, the reduction of computational complexity is achieved only for small variations, giving localized effects.

Practical implications
– The method proposed in the paper can speed up the computations of sensitivity arrays in the robust design and tolerance analysis of electromagnetic device, when numerical methods are applied.

Originality/value
– The use of CT in field computations is not new, but its adoption in the sensitivity computation is new to the best knowledge of authors.