bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tuning the isoelectric point of graphene by electrochemical functionalization
Authors: Zuccaro Laura , Krieg Janina , Desideri Alessandro , Kern Klaus , Balasubramanian Kannan 
Published: July 2015

AbstractThe ability to control the charge-potential landscape at solid-liquid interfaces is pivotal to engineer novel devices for applications in sensing, catalysis and energy conversion. The isoelectric point (pI)/point of zero charge (pzc) of graphene plays a key role in a number of physico-chemical phenomena occurring at the graphene-liquid interface. Supported by theory, we present here a methodology to identify the pI/pzc of (functionalized) graphene, which also allows for estimating the nature and extent of ion adsorption. The pI of bare graphene (as-prepared, chemical vapor deposition (CVD)-grown) is found to be less than 3.3, which we can continuously modify up to 7.5 by non-covalent electrochemical attachment of aromatic amino groups, preserving the favorable electronic properties of graphene throughout. Modelling all the observed results with detailed theory, we also show that specific adsorption of ions and the substrate play only an ancillary role in our capability to tune the pI of graphene.
Lack of an Association between the SDF-1 rs1801157 Polymorphism and Coronary Heart Disease: A Meta-Analysis
Authors: Wu Nan , Zhang Xiaowen , Jia Pengyu , Jia Dalin 
Published: July 2015

AbstractRecent studies have shown that the single-nucleotide polymorphism (SNP) rs1801157 in the stromal cell-derived factor (SDF)-1 gene is associated with susceptibility to coronary heart disease (CHD). However, published studies have shown inconsistent results. Therefore, a meta-analysis was carried out to evaluate the association between rs1801157 and CHD in the literature. A systematic literature search was performed using the PubMed, Web of Science, Cochrane Library, Chinese National Knowledge Infrastructure and Chinese Wan Fang databases. Heterogeneity and publication bias were also evaluated. Seven eligible studies that involved 4656 cases and 2654 controls were finally included in this meta-analysis. Overall, the results showed that the rs1801157 polymorphism was not statistically associated with the risk of CHD under all genetic models but that rs1801157 was associated with decreased susceptibility to myocardial infarction (MI) in subgroup analyses. Moreover, no association was found between rs1801157 and the susceptibility to CHD in either Caucasians or Asians. In conclusion, our meta-analysis demonstrated that the rs1801157 polymorphism is not associated with the susceptibility to CHD but may be associated with a decreased risk of MI. However, further large-scale, case-control studies with rigorous designs should be conducted to confirm these conclusions.
Oil palm deserves government attention in Brazil
Authors: Moreira José R , Goldemberg José 
Published: July 2015

Abstract
Englund et al (2015 Environ. Res. Lett.

10 044002) have recently analyzed biodiesel production from oil palm plantations as one possible way to mitigate climate change while providing cost effective results. They show that data for detailed quantification of biological carbon sequestration is available allowing a high confidence evaluation of positive impacts when oil palm plantation for food and biodiesel production is carried out in degraded, cultivated soil, and also with some varieties of natural vegetation in the Amazon. Nevertheless, economic risk associated with the future price of fossil fuels and uncertainties related with carbon subsidy are barriers. Here we discuss the assumptions under which such controversial proposal is based and suggest further analysis for Brazilian decision makers.
New operator inequalities in finite-dimensional vector spaces
Authors: Gordon Alexander 
Published: July 2015

We establish some new operator inequalities in an

n
n

-dimensional vector space

X
X

equipped with a seminorm

‖
⋅
‖

\|\cdot \|

. Here is an example. If

A
A

is an invertible linear operator in

X
X

and

ξ
\xi

is a vector, then
\[

‖
ξ

‖
r

≤

∑

1
≤

|

j

|

≤

(

n
+
r
−
1

r

)

‖

A
j

ξ

‖
r

.

\|\xi \|^r \le \sum _{1\le |j|\le {n+r-1\choose r}}\|A^j\xi \|^r.

\]
Some special cases have been known and used in mathematical physics.
ISQuest: finding insertion sequences in prokaryotic sequence fragment data
Authors: Biswas Abhishek , Gauthier David T. , Ranjan Desh , Zubair Mohammad 
Published: June 2015

Abstract
Motivation: Insertion sequences (ISs) are transposable elements present in most bacterial and archaeal genomes that play an important role in genomic evolution. The increasing availability of sequenced prokaryotic genomes offers the opportunity to study ISs comprehensively, but development of efficient and accurate tools is required for discovery and annotation. Additionally, prokaryotic genomes are frequently deposited as incomplete, or draft stage because of the substantial cost and effort required to finish genome assembly projects. Development of methods to identify IS directly from raw sequence reads or draft genomes are therefore desirable. Software tools such as Optimized Annotation System for Insertion Sequences and IScan currently identify IS elements in completely assembled and annotated genomes; however, to our knowledge no methods have been developed to identify ISs from raw fragment data or partially assembled genomes. We have developed novel methods to solve this computationally challenging problem, and implemented these methods in the software package ISQuest. This software identifies bacterial ISs and their sequence elements—inverted and direct repeats—in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours, making it a valuable high-throughput tool for a global search of IS elements. We tested ISQuest on simulated read libraries of 3810 complete bacterial genomes and plasmids in GenBank and were capable of detecting 82% of the ISs and transposases annotated in GenBank with 80% sequence identity.
Contact: abiswas@cs.odu.edu
Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level
Authors: Gehrmann Thies , Reinders Marcel J.T. 
Published: June 2015

Abstract
Background: With more and more genomes being sequenced, detecting synteny between genomes becomes more and more important. However, for microorganisms the genomic divergence quickly becomes large, resulting in different codon usage and shuffling of gene order and gene elements such as exons.
Results: We present Proteny, a methodology to detect synteny between diverged genomes. It operates on the amino acid sequence level to be insensitive to codon usage adaptations and clusters groups of exons disregarding order to handle diversity in genomic ordering between genomes. Furthermore, Proteny assigns significance levels to the syntenic clusters such that they can be selected on statistical grounds. Finally, Proteny provides novel ways to visualize results at different scales, facilitating the exploration and interpretation of syntenic regions. We test the performance of Proteny on a standard ground truth dataset, and we illustrate the use of Proteny on two closely related genomes (two different strains of Aspergillus niger) and on two distant genomes (two species of Basidiomycota). In comparison to other tools, we find that Proteny finds clusters with more true homologies in fewer clusters that contain more genes, i.e. Proteny is able to identify a more consistent synteny. Further, we show how genome rearrangements, assembly errors, gene duplications and the conservation of specific genes can be easily studied with Proteny.
Availability and implementation: Proteny is freely available at the Delft Bioinformatics Lab website http://bioinformatics.tudelft.nl/dbl/software.
Contact: t.gehrmann@tudelft.nl
Supplementary information: Supplementary data are available at Bioinformatics online.
Estimating beta diversity for under-sampled communities using the variably weighted Odum dissimilarity index and OTUshuff
Authors: Manter Daniel K. , Bakker Matthew G. 
Published: July 2015

Abstract
Motivation: In profiling the composition and structure of complex microbial communities via high throughput amplicon sequencing, a very low proportion of community members are typically sampled. As a result of this incomplete sampling, estimates of dissimilarity between communities are often inflated, an issue we term pseudo β-diversity.
Results: We present a set of tools to identify and correct for the presence of pseudo β-diversity in contrasts between microbial communities. The variably weighted Odum dissimilarity (DwOdum) allows for down-weighting the influence of either abundant or rare taxa in calculating a measure of similarity between two communities. We show that down-weighting the influence of rare taxa can be used to minimize pseudo β-diversity arising from incomplete sampling. Down-weighting the influence of abundant taxa can increase the sensitivity of hypothesis testing. OTUshuff is an associated test for identifying the presence of pseudo β-diversity in pairwise community contrasts.
Availability and implementation: A Perl script for calculating the DwOdum score from a taxon abundance table and performing pairwise contrasts with OTUshuff can be obtained at http://www.ars.usda.gov/services/software/software.htm?modecode=30-12-10-00.
Contact: daniel.manter@ars.usda.gov
Supplementary information: Supplementary data are available at Bioinformatics online.
An empirical analysis of the financial benefits of health information exchange in emergency departments
Authors: Yaraghi Niam 
Published: June 2015

Abstract
Objective To examine the impact of health information exchange (HIE) on reducing laboratory tests and radiology examinations performed in an emergency department (ED).
Materials and Methods The study was conducted in an ED setting in Western New York over a period of 2 months. The care of the patients in the treatment group included an HIE query for every encounter, while the care of other patients in the control group did not include such queries. A group of medical liaisons were hired to query the medical history of patients from an HIE and provide it to the ED clinicians. Negative binomial regression was used to analyze the effects of HIE queries on the number of performed laboratory tests and radiology examinations. The log files of the HIE system since 1 year before the ED admission were used to analyze the differences in outcome measures between the 2 groups of patients.
Results Ceteris paribus, HIE usage is associated with, respectively, 52% and 36% reduction in the expected total number of laboratory tests and radiology examinations ordered per patient at the ED.
Conclusions The results indicate that access to additional clinical data through the HIE will significantly reduce the number of laboratory tests and radiology examinations performed in the ED settings and thus support the ongoing HIE efforts.
Mitochondrial DNA Copy Number Variation Across Human Cancers
Authors: Reznik Ed , Miller Martin L. , Senbabaoglu Yasin , Riaz Nadeem , Lee William , Sander Chris 
Published: June 2015

AbstractIn cancer, mitochondrial dysfunction, through mutations, deletions, and changes in copy number of mitochondrial DNA (mtDNA), contributes to the malignant transformation and progress of tumors. Here, we report the first large-scale survey of mtDNA copy number variation across 21 distinct solid tumor types, examining over 13,000 tissue samples profiled with next-generation sequencing methods. We find a tendency for cancers, especially of the bladder and kidney, to be significantly depleted of mtDNA, relative to matched normal tissue. We show that mtDNA copy number is correlated to the expression of mitochondrially-localized metabolic pathways, suggesting that mtDNA copy number variation reflect gross changes in mitochondrial metabolic activity. Finally, we identify a subset of tumor-type-specific somatic alterations, including IDH1 and NF1 mutations in gliomas, whose incidence is strongly correlated to mtDNA copy number. Our findings suggest that modulation of mtDNA copy number may play a role in the pathology of cancer.
Comprehensive nucleosome mapping of the human genome in cancer progression
Authors: Druliner Brooke R. , Vera Daniel , Johnson Ruth , Ruan Xiaoyang , Apone Lynne M. , Dimalanta Eileen T. , Stewart Fiona J. , Boardman Lisa , Dennis Jonathan H. 
Published: June 2015

ABSTRACTAltered chromatin structure is a hallmark of cancer, and inappropriate regulation of chromatin structure may represent the origin of transformation. Important studies have mapped human nucleosome distributions genome wide, but the role of chromatin structure in cancer progression has not been addressed. We developed a MNase-Transcription Start Site Sequence Capture method (mTSS-seq) to map the nucleosome distribution at human transcription start sites genome-wide in primary human lung and colon adenocarcinoma tissue. Here, we confirm that nucleosome redistribution is an early, widespread event in lung (LAC) and colon (CRC) adenocarcinoma. These altered nucleosome architectures are consistent between LAC and CRC patient samples indicating that they may serve as important early adenocarcinoma markers. We demonstrate that the nucleosome alterations are driven by the underlying DNA sequence and potentiate transcription factor binding. We conclude that DNA-directed nucleosome redistributions are widespread early in cancer progression. We have proposed an entirely new hierarchical model for chromatin-mediated genome regulation.SignificanceThis is the first report of human nucleosome distribution in cancer progression using sequence capture and HiSeq. We show in lung and colorectal adenocarcinoma patients that nucleosome distribution is a widespread, early response driven by genetically-encoded signals and potentiate regulatory factor binding. We present a model for chromatin-based hierarchical regulation.
Origins of cell-to-cell variability, kinetic proof-reading and the robustness of MAPK signal transduction
Authors: Filippi Sarah , Barnes Chris P. , Kirk Paul , Kudo Takamasa , McMahon Siobhan , Tsuchiya Takaho , Wada Takumi , Kuroda Shinya , Stumpf Michael P.H. 
Published: July 2015

SummaryCellular signalling processes can exhibit pronounced cell-to-cell variability in genetically identical cells. This affects how individual cells respond differentially to the same environmental stimulus. However, the origins of cell-to-cell variability in cellular signalling systems remain poorly understood. Here we measure the temporal evolution of phosphorylated MEK and ERK dynamics across populations of cells and quantify the levels of population heterogeneity over time using high-throughput image cytometry. We use a statistical modelling framework to show that upstream noise is the dominant factor causing cell-to-cell variability in ERK phosphorylation, rather than stochasticity in the phosphorylation/dephosphorylation of ERK. In particular, the cell-to-cell variability during sustained phosphorylation stems from random fluctuations in the background upstream signalling processes, while during transient phosphorylation, the heterogeneity is primarily due to noise in the intensity of the upstream signal(s). We show that the core MEK/ERK system uses kinetic proof-reading to faithfully and robustly transmits these variable inputs. The MAPK cascade thus propagates cell-to-cell variability at the population level, rather than attenuating or increasing it.
Design optimization for cogging torque mitigation in brushless DC motor using multi-objective particle swarm optimization algorithm
Authors: Nagalingam Umadevi , Mahadevan Balaji , Vijayarajan Kamaraj , Loganathan Ananda Padmanaban 
Published: July 2015

Purpose– The purpose of this paper is to propose a multi-objective particle swarm optimization (MOPSO) algorithm based design optimization of Brushless DC (BLDC) motor with a view to mitigate cogging torque and enhance the efficiency.Design/methodology/approach– The suitability of MOPSO algorithm is tested on a 120 W BLDC motor considering magnet axial length, stator slot opening and air gap length as the design variables. It avails the use of MagNet 7.5.1, a Finite Element Analysis tool, to account for the geometry and the non-linearity of material for assuaging an improved design framework and operates through the boundaries of generalized regression neural network (GRNN) to advocate the optimum design. The results of MOPSO are compared with Multi-Objective Genetic Algorithm and Non-dominated Sorting Genetic Algorithm-II based formulations for claiming its place in real world applications.Findings– A MOPSO design optimization procedure has been enlivened to escalate the performance of the BLDC motor. The optimality in design has been out reached through minimizing the cogging torque, maximizing the average torque and reducing the total losses to claim an increase in the efficiency. The results have been fortified in well-distributed Pareto-optimal planes to arrive at trade-off solutions between different objectives.Research limitations/implications– The rhetoric theory of multi objective formulations has been reinforced to provide a decisive solution with regard to the choice of the design obtained from Pareto-optimal planes.Practical implications– The incorporation of a larger number of design variables together with an orientation to thermal and vibration analysis will still go a long way in bringing on board new dimensions to the fold of optimality in the design of BLDC motors.Originality/value– The proposal offers a new perspective to the design of BLDC motor in the sense it be-hives the facility of a swarm based approach to optimize the parameters in order that it serves to improve its performance. The results of a 120 W motor in terms of lowering the losses, minimizing the cogging torque and maximizing the average torque emphasize the benefits of the GRNN based multi-objective formulation and establish its viability for use in practical applications.
Compulsive buying: the role of earlier-in-life events and experiences
Authors: Grougiou Vassiliki , Moschis George , Kapoutsis Ilias 
Published: July 2015

Purpose– This study aims to examine the effects of earlier-in-life family events and experiences on the development of compulsive buying behavior in later life.Design/methodology/approach– The study is based on data collected from a self-administered survey of 285 young Greek adults.Findings– Young individuals appear to be particularly susceptible to their peers’ evaluations of consumption matters. However, those who experience family disruptions and have a low socio-economic status are least likely to communicate with their peers about consumer matters, possibly as a self-protection coping mechanism. Contrary to previous findings, family communication styles promote rather than deter the development of compulsive tendencies, suggesting the influence of other macro-environmental factors upon the development of young adults’ compulsive consumption tendencies.Social implications– Understanding the underlying mechanisms and contexts that promote the development of compulsive buying is imperative for deterring the onset of maladaptive consumption habits that have adverse effects on the individual and on society as a whole.Originality/value– Using the multi-theoretical life course paradigm, this study highlights the links between earlier-in-life experiences and social contexts to the onset and development of compulsive behaviors. The findings could assist public policy makers and parents to use strategies that would educate and protect future generations from developing compulsive consumption habits.
When face engulfs the field: differential effects of visual quality levels in print ads
Authors: Kergoat Marine , Meyer Thierry 
Published: July 2015

Purpose
– This study aims to examine the influence of a visual alteration in print advertising on viewers’ responses according to the different textual and pictorial information contained in the ad.

Design/methodology/approach
– Through an experimental design, the presence or not of a human face and the kind of verbal claims (self-centered vs product-centered) were manipulated, as well as visual fluency manipulated by varying the clarity of the ads.

Findings
– As expected, the presence of a human face, as opposed to just a product picture, has led to stronger negative effects on attitudes and purchase intention when the ad was visually altered. In addition, ad’s claim directed toward the self yielded lower purchase intentions compared to arguments directed toward product characteristics. Findings supported our main expectations, but also demonstrated contrasted effect, plausibly due to a bias correction.

Research limitations/implications
– To comfort these findings, further research should be realized on other advertising varying the kind of human face stimuli (e.g. woman/man; smiling/neutral; beautiful/average).

Practical implications
– In terms of practical implications, it highlights the significance of considering the medium of communication used for print ads with caution. The pictorial use of a human face can be particularly harmful in the persuasive process if there is a risk that the ad could be visually altered.

Originality/value
– Currently, little is known about how sub-optimal visual exposition changes attitudes and behaviors depending on the content of an ad. The present study expands research on processing fluency effects and the use of models in advertisements.
The role of MNCs and information flow on institutional change
Authors: Kalliny Morris , Benmamoun Mamoun , Cropf Robert A. , Kim Seung H. 
Published: July 2015

Purpose– The purpose of this paper is to investigate the impact of large business corporations, particularly media corporations, such as television (e.g. satellite networks), newspapers and social media (e.g. Facebook), on institutional change in the Arab world, which directly impact political and civil liberties in the region.Design/methodology/approach– Although there are several methods to measure institutional change, this paper relied on Kaufmannet al.(2010)’s governance indicators that capture, historically, how authority is exercised in a nation state. As the focus of this paper is on how information flows have empowered citizens in the Arab world, we built a panel database around one relevant governance indicator: “Voice and Accountability”. As a measure of governance, “Voice and Accountability” summarizes the condition of political, civil and human rights such as freedom of expression and freedom of association in a given country. This indicator takes scores ranging from 2.5, corresponding to strong governance, to −2.5, corresponding to weak governance.Findings– As predicted, the information flows variable has a positive and significant effect on institutional change. Table II also suggests that political globalization has a positive and significant effect on institutional change in the Arab world. In contrast, the variables for cultural proximity and human capital are associated with negative effects on institutional change.Originality/value– This paper is unique in the sense that it tackles a growing trend in the Arab world, namely, the impact of media on institutions.