bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlled morphology and optical properties of n-type porous silicon: effect of magnetic field and electrode-assisted LEF
Authors: Antunez Edgar E , Campos Jose , Basurto Miguel A , Agarwal Vivechana 
Published: September 2014

Abstract
Fabrication of photoluminescent n-type porous silicon (nPS), using electrode-assisted lateral electric field accompanied with a perpendicular magnetic field, is reported. The results have been compared with the porous structures fabricated by means of conventional anodization and electrode-assisted lateral electric field without magnetic field. The lateral electric field (LEF) applied across the silicon substrate leads to the formation of structural gradient in terms of density, dimension, and depth of the etched pores. Apart from the pore shape tunability, the simultaneous application of LEF and magnetic field (MF) contributes to a reduction of the dimension of the pores and promotes relatively more defined pore tips as well as a decreased side-branching in the pore walls of the macroporous structure. Additionally, when using magnetic field-assisted etching, within a certain range of LEF, an enhancement of the photoluminescence (PL) response was obtained.
Arima hot spring waters as a deep-seated brine from subducting slab
Authors: Kusuda Chiho , Iwamori Hikaru , Nakamura Hitomi , Kazahaya Kohei , Morikawa Noritoshi 
Published: September 2014

Abstract
Non-volcanic hot springs are generally believed to originate through circulation of meteoric or buried sea water heated at depth. In this study, we report the geochemical characteristics of the Arima and Takarazuka hot spring waters, known as Arima-type deep brine, in a forearc region of southwestern Japan. We examine 14 water samples to determine the levels of 12 solute elements or components and the isotopic ratios of H, He, C, O, and Sr, and we perform correlation analysis of the data to deduce the source materials and origin of the deep brine. Moreover, we perform numerical modeling of oxygen and hydrogen isotopic fractionation along subducting slabs to examine the composition of slab-derived fluid as a possible candidate of the deep brine. The results suggest that the high salinity and solute concentrations with characteristic oxygen, hydrogen, carbon, and strontium isotope compositions, as well as high 3He/4He ratios, can be explained by a dehydrated component of the subducted Philippine Sea slab. Hence, this study may provide an invaluable understanding of geofluid processes over a significant depth range.
Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies
Authors: Panousis Nikolaos I , Gutierrez-Arcelus Maria , Dermitzakis Emmanouil T , Lappalainen Tuuli 
Published: September 2014

Abstract
Background
RNA sequencing (RNA-seq) is the current gold-standard method to quantify gene expression for expression quantitative trait locus (eQTL) studies. However, a potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias gene quantifications and cause false positive eQTL associations. In this study, we analyze the effect of this allelic mapping bias in eQTL discovery.

Results
We simulate RNA-seq read mapping over 9.5 M common SNPs and indels, with 15.6% of variants showing biased mapping rate for reference versus non-reference reads. However, removing potentially biased RNA-seq reads from an eQTL dataset of 185 individuals has a very small effect on gene and exon quantifications and eQTL discovery. We detect only a handful of likely false positive eQTLs, and overall eQTL SNPs show no significant enrichment for high mapping bias.

Conclusion
Our results suggest that RNA-seq quantifications are generally robust against allelic mapping bias, and that this does not have a severe effect on eQTL discovery. Nevertheless, we provide our catalog of putatively biased loci to allow better controlling for mapping bias to obtain more accurate results in future RNA-seq studies.
Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes
Authors: Blattler Adam , Yao Lijing , Witt Heather , Guo Yu , Nicolet Charles M , Berman Benjamin P , Farnham Peggy J 
Published: September 2014

Abstract
Background
Gene expression is epigenetically regulated by a combination of histone modifications and methylation of CpG dinucleotides in promoters. In normal cells, CpG-rich promoters are typically unmethylated, marked with histone modifications such as H3K4me3, and are highly active. During neoplastic transformation, CpG dinucleotides of CG-rich promoters become aberrantly methylated, corresponding with the removal of active histone modifications and transcriptional silencing. Outside of promoter regions, distal enhancers play a major role in the cell type-specific regulation of gene expression. Enhancers, which function by bringing activating complexes to promoters through chromosomal looping, are also modulated by a combination of DNA methylation and histone modifications.

Results
Here we use HCT116 colorectal cancer cells with and without mutations in DNA methyltransferases, the latter of which results in a 95% reduction in global DNA methylation levels. These cells are used to study the relationship between DNA methylation, histone modifications, and gene expression. We find that the loss of DNA methylation is not sufficient to reactivate most of the silenced promoters. In contrast, the removal of DNA methylation results in the activation of a large number of enhancer regions as determined by the acquisition of active histone marks.

Conclusions
Although the transcriptome is largely unaffected by the loss of DNA methylation, we identify two distinct mechanisms resulting in the upregulation of distinct sets of genes. One is a direct result of DNA methylation loss at a set of promoter regions and the other is due to the presence of new intragenic enhancers.
PAGAL - Properties and corresponding graphics of alpha helical structures in proteins
Authors: Chakraborty Sandeep , Rao Basuthkar J. , Dandekar Abhaya M. 
Published: September 2014

Alpha helices (AH) are peptide fragments characterized by regular patterns of hydrogen bonding between the carbonyl oxygen and amino nitrogen of residues regularly spaced in sequence, resulting in spiral conformations. Their preponderance in protein structures underlines their importance. Interestingly, AHs are present in most anti-microbial peptides, although they might remain in random-coil conformations depending on the solvent dielectric. For example, the cecropin component of the chimeric anti-microbial protein designed previously by our group comprises of two AHs linked by a short stretch of random coil. These anti-microbial peptides are often amphipathic (quantified by a hydrophobic moment), aligning hydrophobic residues on one surface and charged residues on the others. In the current work, we reproduce previously described computational methods to compute the hydrophobic moment of AHs - and provide open access to the source code (PAGAL). We simultaneously generated input files for TikZ (a package for creating high resolution graphics programmatically) to obtain the Edmundson wheel and showing the direction and magnitude of the hydrophobic moment, and Pymol scripts to generate color coded protein surfaces. Additionally, we have observed an empirical structural property of AHs: the distance between the Cα atoms of the ith and (i+4)th residue is equal to the distance between the carbonyl oxygens of the ith and (i+4)th residue. We validated this using 100 non-homologous high resolution structures from the PISCES database. The source code and manual is available at http://github.com/sanchak/pagal and on http://dx.doi.org/10.5281/zenodo.11136.
Value-in-Context of Healthcare: What Human Factors Differentiate Quality of Nursing Services?
Authors: Matsushita Hironobu , Kijima Kyoichi 
Published: September 2014

With social issues such as an aging society and the sustainability of health service systems becoming of greater concern, decision makers in health service sectors need to identify the human factors that differentiate the performance of health service professionals such as nurses. However, the fact remains that a nursing shortage has hindered such efforts in many countries. What brings about value in nursing services? How is value cocreated in clinical settings by nurses, patients, and other agents? Given that service is the application of competencies for the benefit of another entity, this work is an attempt to identify the typology of competencies as operant resources where value is idiosyncratic, experiential, contextual, and meaning-laden. In so doing, this paper explores meaningful relations among service quality, human competency, and contextualization. Therefore, the objective of this study, conducted in one of the leading university hospitals that employs 1,448 nurses, and with the support of the Japanese government, was to identify the characteristics of human activity systems, focusing on the relationships between service quality, human competency, and value-in-context. This work used the original transcript text obtained by combining the critical incident technique and behavioral event interview approaches. After collecting qualitative data, text coding was performed on the interview transcripts. The findings of the present work contribute to practitioners and theoreticians by providing a bridging concept between human resources management and service systems management. First, our ethnographical research reveals that nurses in different role groups applied different sets of competencies in their diverse job contexts, where there exist commonly applied differentiating competencies as well as other threshold competencies. Second, in an attempt to explore the features of value cocreation, this paper explores the relationship between competencies in action and dynamic contexts translation. Third, to address value cocreation systems in value-in-contexts focusing on nursing and caring services, this paper proposes a meta value-in-context translational model.
Cyclic compressive loading on 3D tissue of human synovial fibroblasts upregulates prostaglandin E2 via COX-2 production without IL-1β and TNF-α
Authors: Shimomura K. , Kanamoto T. , Kita K. , Akamine Y. , Nakamura N. , Mae T. , Yoshikawa H. , Nakata K. 
Published: September 2014

ObjectiveExcessive mechanical stress on synovial joints causes osteoarthritis (OA) and results in the production of prostaglandin E2 (PGE2), a key molecule in arthritis, by synovial fibroblasts. However, the relationship between arthritis-related molecules and mechanical stress is still unclear. The purpose of this study was to examine the synovial fibroblast response to cyclic mechanical stress using an in vitro osteoarthritis model.MethodHuman synovial fibroblasts were cultured on collagen scaffolds to produce three-dimensional constructs. A cyclic compressive loading of 40 kPa at 0.5 Hz was applied to the constructs, with or without the administration of a cyclooxygenase-2 (COX-2) selective inhibitor or dexamethasone, and then the concentrations of PGE2, interleukin-1β (IL-1β), tumour necrosis factor-α (TNF-α), IL-6, IL-8 and COX-2 were measured.ResultsThe concentrations of PGE2, IL-6 and IL-8 in the loaded samples were significantly higher than those of unloaded samples; however, the concentrations of IL-1β and TNF-α were the same as the unloaded samples. After the administration of a COX-2 selective inhibitor, the increased concentration of PGE2 by cyclic compressive loading was impeded, but the concentrations of IL-6 and IL-8 remained high. With dexamethasone, upregulation of PGE2, IL-6 and IL-8 was suppressed.ConclusionThese results could be useful in revealing the molecular mechanism of mechanical stress in vivo for a better understanding of the pathology and therapy of OA. Cite this article: Bone Joint Res 2014;3:280–8.
The Current State of Resident Training in Genomic Pathology
Authors: Haspel Richard L. , Rinder Henry M. , Frank Karen M. , Wagner Jay , Ali Asma M. , Fisher Patrick B. , Parks Eric R. 
Published: September 2014

Abstract

Objectives:
To determine the current state of pathology resident training in genomic and molecular pathology.

Methods:
The Training Residents in Genomics (TRIG) Working Group developed survey and knowledge questions for the 2013 pathology Resident In-Service Examination (RISE). Sixteen demographic questions related to amount of training, current and predicted future use, and perceived ability in molecular pathology vs genomic medicine were included, along with five genomic pathology and 19 molecular pathology knowledge questions.

Results:
A total of 2,506 pathology residents took the 2013 RISE, with approximately 600 individuals per postgraduate year (PGY). For genomic medicine, 42% of PGY-4 respondents stated they had no training, compared with 7% for molecular pathology (P &lt; .001). PGY-4 residents’ perceived ability, comfort in discussing results, and predicted future use as a practicing pathologist were reported to be less in genomic medicine than in molecular pathology (P &lt; .001). Based on PGY, knowledge question scores showed a greater increase in molecular pathology than in genomic pathology.

Conclusions:
The RISE is a powerful tool for assessing the state of resident training in genomic pathology and current results suggest a significant deficit. The results also provide a baseline to assess future initiatives to improve genomics education for pathology residents such as those developed by the TRIG Working Group.
A new species of phyllophoracean red algae (Gigartinales, Rhodophyta) from Korea: Stenogramma guleopensis sp. nov.
Authors: Calderon Martha S. , Boo Sung Min 
Published: September 2014

Abstract
The occurrence of Stenogramma interruptum in northeast Asian waters is a matter of debate. We analyzed rbcL from Korean specimens filed under the species name S. interruptum in combination with morphological observations. A partial rbcL sequence revealed that the Korean specimens were clearly distinct from other species of Stenogramma as well as S. interruptum from Europe. The morphology and anatomy of the Korean specimens were consistent with the rbcL data. Based on these results, we herein describe the new species Stenogramma guleopensis from Korea. Stenogramma guleopensis is distinguished mostly by its small size (up to 8 cm), slender thallus with narrow and parallel-sided segments, terminal branches basally constricted, two layers of cortical cells, two to three layers of medullary cells, and a gradient of two layers of smaller cells between the cortex and medulla. Further collections and careful examinations in the field will probably reveal extension of the distribution of S. guleopensis to the waters surrounding Korea.
Piecewise Cause-Specific Association Analyses of Multivariate Untied or Tied Competing Risks Data
Authors: Wang Hao , Cheng Yu 
Published: September 2014

AbstractIn this paper we extend the bivariate hazard ratio to multivariate competing risks data and show that it is equivalent to the cause-specific cross hazard ratio. Two approaches are proposed to estimate these two equivalent association measures. One extends the plug-in estimator, and the other adapts the pseudo-likelihood estimator for bivariate survival data to multivariate competing risks data. The asymptotic properties of the extended estimators are established by using empirical processes techniques. The extended plug-in and pseudo-likelihood estimators have comparable performance with the existing U-statistic when the data have no tied events. However, in many applications, there are tied events in which all the three estimators are found to produce biased results. To our best knowledge, we are not aware of any association analysis for multivariate competing risks data that has considered tied events. Hence we propose a modified U-statistic to specifically handle tied observations. The modified U-statistic clearly outperforms the other estimators when there are rounding errors. All methods are applied to the Cache County Study to examine mother–child and sibship associations in dementia among this aging population, where the event times are rounded to the nearest integers. The modified U performs consistently with our simulation results and provides more reliable results in the presence of tied events.
Efficient Algorithms for Mining Frequent Patterns from Sparse and Dense Databases
Authors: Vu Lan , Alaghband Gita 
Published: September 2014

AbstractIn this article, we present a new approach for frequent pattern mining (FPM) that runs fast for both sparse and dense databases. Two algorithms, FEM and DFEM, based on our approach are also introduced. FEM applies a fixed threshold as the condition for switching between the two mining strategies; meanwhile, DFEM adopts this threshold dynamically at runtime to best fit the characteristics of the database during the mining process, especially when minimum support threshold is low. Additionally, we present optimization techniques for the proposed algorithms to speed the mining process, reduce the memory usage, and optimize the I/O cost. We also analyze in depth the performance of FEM and DFEM and compare them with several existing algorithms. The experimental results show that FEM and DFEM achieve a significant improvement in execution time and consume less memory than many popular FPM algorithms including the well-known Apriori, FP-growth, and Eclat.
Polymer engineering for drug/gene delivery: from simple towards complex architectures and hybrid materials
Authors: David Geta , Fundueanu Gheorghe , Pinteala Mariana , Minea Bogdan , Dascalu Andrei , Simionescu Bogdan C. 
Published: September 2014

Abstract
The paper summarizes the history of the drug/gene delivery domain, pointing on polymers as a solution to specific challenges, and outlines the current situation in the field – focusing on the newest strategies intended to improve systems effectiveness and responsiveness (design keys, preparative approaches). Some recent results of the authors are briefly presented.
Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains
Authors: Wilson Catherine A , High Samantha K , McCluskey Braedan M , Amores Angel , Yan Yi-lin , Titus Tom A , Anderson Jennifer L , Batzel Peter , Carvan Michael J , Schartl Manfred , Postlethwait John H 
Published: September 2014

AbstractSex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this “RAD-sex” method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, “male genotypes” became males and some “female genotypes” also became males, suggesting that the environment or genetic background can cause female-to-male sex reversal. Surprisingly, TU and AB lacked detectable sex-linked loci. Phylogenomics rooted on D. nigrofasciatus verified that all strains are monophyletic. Because AB and TU branched as a monophyletic clade, we could not rule out shared loss of the wild sex locus in a common ancestor despite their independent domestication. Mitochondrial DNA sequences showed that investigated strains represent only one of the three identified zebrafish haplogroups. Results suggest that zebrafish in nature possess a WZ/ZZ sex-determination mechanism with a major determinant lying near the right telomere of chromosome 4 that was modified during domestication. Strains providing the zebrafish reference genome lack key components of the natural sex-determination system but may have evolved variant sex-determining mechanisms during two decades in laboratory culture.
Deciduous teeth structure changes in congenital heart disease: Ultrastructure and microanalysis
Authors: El-Hawary Yousry M. , El-Sayed Basmah , Abd-Alhakem Gehan , Ibrahim Fatma M. 
Published: September 2014

Abstract

Objectives
Oral manifestations recorded for congenital heart disease (CHD) patients include teeth hypoplasia and high caries incidence. These observations suggested that the enamel and dentin of the teeth may be altered, increasing the risk for caries incidence. This study was designed to investigate the eff ect of CHD on the ultrastructure and composition of deciduous sound teeth.

Methods
Thirty sound exfoliated human deciduous incisor teeth were selected for this study. They were divided into three groups, Group I (control) from healthy children (n = 6), Group II from acyanotic CHD children (n = 12) and Group III from cyanotic CHD children (n = 12). Each tooth was longitudinally sectioned, providing enough specimens for ultrastructure and chemical analysis using ESEM/EDAX. The results of ESEM/EDAX and dentin image analysis were statistically analyzed using one-way ANOVA test followed by Tukey's test.

Results
Enamel of groups II and III showed increased dissolution and irregular orientation of enamel prisms. Orifices of dentinal tubules demonstrated widening and irregular outlines, also lateral branching increased markedly. Image analysis of dentin ESEM photomicrographs showed a highly significant increase in surface area of dentinal tubules. Decrease in calcium (Ca) and phosphorus (P) levels was statistically significant (P < 0.05).

Conclusions
CHDs affect the structure and chemical composition of deciduous teeth.
Innovative In-Situ Remedial Technologies for Petroleum Hydrocarbon Remediation
Authors: Ayyaswami Arul 
Published: September 2014

Abstract
INNOVATIVE IN-SITU REMEDIAL TECHNOLOGIES FOR PETROLEUM HYDROCARBON REMEDIATION
A Presentation by
Arul Ayyaswami, Vice-President Tetra Tech, Langhorne, PA
Innovative in-situ technologies have been implemented in the United States and the Western European countries to cost effectively treat the petroleum hydrocarbons in the sub-surface. These technologies are not only cheaper, but also effectively remove the mass faster than conventional treatment technologies for soil and groundwater treatment.