bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remission of severe aphthous stomatitis of celiac disease with etanercept
Authors: Hasan Adey , Patel Hiren , Saleh Hana , Youngberg George , Litchfield John , Krishnaswamy Guha 
Published: December 2013

Abstract
Celiac disease is a common autoimmune disease triggered by gluten-containing foods (wheat, barley and rye) in genetically predisposed individuals. We present a patient with celiac disease complicated by severe aphthous stomatitis resulting in impairing swallowing, chewing and speaking. This led to weight loss, psychosocial problems as well as inability to perform her work. A variety of topical and systemic medications used resulted in either no improvement or only partial alleviation of the patient’s symptoms. After informed consent, etanercept was initiated and resulted in complete remission of aphthous stomatitis, decrease in arthralgia and fatigue and considerable improvement in her quality of life. The use of newer biological agents for selected and severe manifestations of celiac disease may lead to improved morbidity in these patients, but more studies are needed to determine long-term efficacy as well as safety of these drugs in the mucosal and/or systemic complications of this disease.
Architecture of epigenetic reprogramming following Twist1-mediated epithelial-mesenchymal transition
Authors: Malouf Gabriel G , Taube Joseph H , Lu Yue , Roysarkar Tapasree , Panjarian Shoghag , Estecio Marcos RH , Jelinek Jaroslav , Yamazaki Jumpei , Raynal Noel J-M , Long Hai , Tahara Tomomitsu , Tinnirello Agata , Ramachandran Priyanka , Zhang Xiu-Ying , Liang Shoudan , Mani Sendurai A , Issa Jean-Pierre J 
Published: December 2013

Abstract
Background
Epithelial-mesenchymal transition (EMT) is known to impart metastasis and stemness characteristics in breast cancer. To characterize the epigenetic reprogramming following Twist1-induced EMT, we characterized the epigenetic and transcriptome landscapes using whole-genome transcriptome analysis by RNA-seq, DNA methylation by digital restriction enzyme analysis of methylation (DREAM) and histone modifications by CHIP-seq of H3K4me3 and H3K27me3 in immortalized human mammary epithelial cells relative to cells induced to undergo EMT by Twist1.

Results
EMT is accompanied by focal hypermethylation and widespread global DNA hypomethylation, predominantly within transcriptionally repressed gene bodies. At the chromatin level, the number of gene promoters marked by H3K4me3 increases by more than one fifth; H3K27me3 undergoes dynamic genomic redistribution characterized by loss at half of gene promoters and overall reduction of peak size by almost half. This is paralleled by increased phosphorylation of EZH2 at serine 21. Among genes with highly altered mRNA expression, 23.1% switch between H3K4me3 and H3K27me3 marks, and those point to the master EMT targets and regulators CDH1, PDGFRα and ESRP1. Strikingly, Twist1 increases the number of bivalent genes by more than two fold. Inhibition of the H3K27 methyltransferases EZH2 and EZH1, which form part of the Polycomb repressive complex 2 (PRC2), blocks EMT and stemness properties.

Conclusions
Our findings demonstrate that the EMT program requires epigenetic remodeling by the Polycomb and Trithorax complexes leading to increased cellular plasticity. This suggests that inhibiting epigenetic remodeling and thus decrease plasticity will prevent EMT, and the associated breast cancer metastasis.
Determinants of Pain Severity Changes in Ambulatory Patients With Cancer: An Analysis From Eastern Cooperative Oncology Group Trial E2Z02
Authors: Zhao Fengmin , Chang Victor T. , Cleeland Charles , Cleary James F. , Mitchell Edith P. , Wagner Lynne I. , Fisch Michael J. 
Published: December 2013

Purpose To understand changes in pain severity over time and to explore the factors associated with pain changes in ambulatory patients with solid tumors. Patients and Methods We enrolled 3,106 patients with invasive cancer of the breast, prostate, colon/rectum, or lung from multiple sites. At baseline and 4 to 5 weeks later, patients rated their pain level on a 0 to 10 numerical rating scale. A 2-point change in pain score was defined as a clinically significant change in pain. Multivariable logistic models were fitted to examine the effects of pain management and demographic and clinical factors on change in pain severity. Results We analyzed 2,761 patients for changes in pain severity. At initial assessment, 53.0% had no pain, 23.5% had mild pain, 10.3% had moderate pain, and 13.2% had severe pain. Overall, one third of patients with initial pain had pain reduction within 1 month of follow-up, and one fifth had an increase, and the improvement and worsening of pain varied by baseline pain score. Of the patients without pain at initial assessment, 28.4% had pain (8.9% moderate to severe) at the follow-up assessment. Logistic regression analysis showed that inadequate pain management was significantly associated with pain deterioration, as were lower baseline pain level, younger age, and poor health status. Conclusion One third of patients have pain improvement and one fifth experience pain deterioration within 1 month after initial assessment. Inadequate pain management, baseline pain severity, and certain patient demographic and disease characteristics are associated with pain deterioration.
Plasma fetuin-A levels are reduced in patients with hypothyroidism
Authors: Bakiner Okan , Bozkirli Emre , Ertugrul Derun , Sezgin Nurzen , Ertorer Eda 
Published: December 2013

ObjectiveTo determine plasma fetuin-A levels in hypothyroid patients before and after treatment withl-thyroxine (T4) and to determine the relation between plasma fetuin-A levels with cardiovascular risk factors.DesignA prospective, controlled, single-blind study.MethodsForty-four treatment-naive female patients diagnosed with hypothyroidism and 39 age- and sex-matched control subjects were enrolled. Anthropometric measurements, blood pressure, plasma TSH, fetuin-A, free T4, LDL-cholesterol, triglyceride, C-reactive protein, fibrinogen levels, and brachial artery flow-mediated dilatation were measured. All measurements were repeated after 3 months in the control group and 3 months after the attainment of euthyroidism withl-T4replacement in the hypothyroid group.Baseline data were compared between the two groups. Posttreatment plasma fetuin-A levels of hypothyroid patients were compared with baseline levels of both groups. The relationship between plasma fetuin-A, TSH levels, and other cardiovascular risk factors was evaluated.ResultsPlasma fetuin-A levels were ∼20% lower in hypothyroid female patients compared with the controls (P=0.0001). Fetuin-A levels increased by ∼20% in hypothyroid patients after achievement of euthyroidism (P=0.0001) and were no longer different compared with controls (P=0.38). There was a negative correlation between plasma TSH and fetuin-A levels (r=−0.79;P=0.001). There was no significant correlation between plasma fetuin-A levels and cardiovascular risk factors within or between groups. The fetuin-A levels were normalized with thyroid hormone treatment.ConclusionPlasma fetuin-A levels are reduced in female patients with hypothyroidism, which are restored to normal during restoration of euthyroidism. There was no relation with cardiovascular risk factors.
Large-Scale Quality Analysis of Published ChIP-seq Data
Authors: Marinov Georgi K , Kundaje Anshul , Park Peter J , Wold Barbara J 
Published: December 2013

Abstract
ChIP-seq has become the primary method for identifying in vivo protein–DNA interactions on a genome-wide scale, with nearly 800 publications involving the technique appearing in PubMed as of December 2012. Individually and in aggregate, these data are an important and information-rich resource. However, uncertainties about data quality confound their use by the wider research community. Recently, the Encyclopedia of DNA Elements (ENCODE) project developed and applied metrics to objectively measure ChIP-seq data quality. The ENCODE quality analysis was useful for flagging datasets for closer inspection, eliminating or replacing poor data, and for driving changes in experimental pipelines. There had been no similarly systematic quality analysis of the large and disparate body of published ChIP-seq profiles. Here, we report a uniform analysis of vertebrate transcription factor ChIP-seq datasets in the Gene Expression Omnibus (GEO) repository as of April 1, 2012. The majority (55%) of datasets scored as being highly successful, but a substantial minority (20%) were of apparently poor quality, and another ∼25% were of intermediate quality. We discuss how different uses of ChIP-seq data are affected by specific aspects of data quality, and we highlight exceptional instances for which the metric values should not be taken at face value. Unexpectedly, we discovered that a significant subset of control datasets (i.e., no immunoprecipitation and mock immunoprecipitation samples) display an enrichment structure similar to successful ChIP-seq data. This can, in turn, affect peak calling and data interpretation. Published datasets identified here as high-quality comprise a large group that users can draw on for large-scale integrated analysis. In the future, ChIP-seq quality assessment similar to that used here could guide experimentalists at early stages in a study, provide useful input in the publication process, and be used to stratify ChIP-seq data for different community-wide uses.
Genomic Characterization of the Mouse Ribosomal DNA Locus
Authors: Zentner Gabriel E , Balow Stephanie A , Scacheri Peter C 
Published: December 2013

Abstract
The transcription of rRNA is critical to all living cells and is tightly controlled at the level of chromatin structure. Although the widespread adoption of genomic technologies including chromatin immunoprecipitation with massively parallel short-read sequencing (ChIP-seq) has allowed for the interrogation of chromatin structure on a genome-wide scale, until recently rDNA has not been analyzed by this technique. We extended genomic analysis of rDNA to mouse (Mus musculus), in which rDNA is similar in structure but highly divergent in sequence compared with human rDNA. Comparison of rDNA histone marks between mouse embryonic stem cells (mESCs) and more differentiated mouse cell types revealed differences between pluripotent and differentiated states. We also observed substantial divergence in rDNA histone modification patterns between mESCs and human embryonic stem cells (hESCs). Surprisingly, we found that the pluripotency factor OCT4 was bound to rDNA in similar patterns in mESCs and hESCs. Extending this analysis, we found that an additional 17 pluripotency-associated factors were bound to rDNA in mESCs, suggesting novel modes of rDNA regulation in pluripotent cells. Taken together, our results provide a detailed view of rDNA chromatin structure in an important model system and enable high-resolution comparison of rDNA regulation between mouse and human.
Effect of Microbial (Jeevatu) Treatment on Rice (Oryza sativa L.) Production
Authors: Adhikari Suraj Raj , Paudel Khadga Bhakta , Pokhrel Kusum , Paudel Amrita 
Published: December 2013

JeevatuTM is a consortium of beneficial natural microbes, available in liquid form. The yield of rice was observed vigorously high in Jeevatu based rice cultivated plant. The seed production in per spikelet is 237.1±44.92 in Jeevatu based and 179.4±25.26 in chemical based rice plant. In case of vegetative growth, 173.1±6.34 cm and 140.9±11.11 cm in Jeevatu based rice plant and chemical based methods respectively. Similarly the length of stalk of spikelet is 27±1.63cm and 22.1±2.23 cm was observed in Jeevatu based and chemical based respectively. The number of stalk in lumps is 16.2±1.75 and 12.2±2.20 in Jeevatu and chemical based paddy plant respectively under the same environment and physical factors.DOI: http://dx.doi.org/10.3126/ijasbt.v1i4.9134 Int J Appl Sci Biotechnol, Vol. 1(4): 184-188
Synthesis, Characterization and Biocidal Evaluation of Azole-Based Ligandsmetal Complexes
Authors: Olagboye S. A. , Hassan G. F. 
Published: December 2013

Different metal complexes of the azole-based ligands have been synthesized and characterized based on the solubility, percentage yield, melting points and conductivity a well as the antimicrobial evaluations on the selected fungi species of plant pathogens. The studies revealed that solid metal complexes were soluble in 80% water and 20% (DMSO) dimethylsulphuroxide and the percentage yields were of appreciable high while the conductivity results showed that metal complexes were non-electrolytes. The solid complexes were also screened against the fungi species: Rhizoctonia solani,Pythium aphaindermatum,Rhizoctonia cerealis,Sclerotium rofisil ,Phyphotoria palmivora (causative agent of black pod diseases) and Benlate a commercial anti fungi agent (as control).The results of the present studies confirmed that metal complexes had good inhibitory actions on the growth of the fungi species and metal complexes appeared to be more proactive on the tested organisms than the free ligands.DOI: http://dx.doi.org/10.3126/ijasbt.v1i4.9176 Int J Appl Sci Biotechnol, Vol. 1(4): 258-265
Thermal, mechanical, and gas barrier properties of ethylene–vinyl alcohol copolymer‐based nanocomposites for food packaging films: Effects of nanoclay loading
Authors: Kim Seong Woo , Cha Sang‐Ho 
Published: December 2013

AbstractFor the application of single‐layer food packaging films with improved barrier properties, an attempt was made to prepare ethylene‐vinyl alcohol (EVOH) copolymer‐based nanocomposite films by incorporation of organically modified montmorillonite nanoclays via a two‐step mixing process and solvent cast method. The highly intercalated tactoids coexisted with exfoliated clay nanosheets, and the extent of intercalation and exfoliation depended significantly on the level of clay loadings, which were confirmed from both XRD measurements and TEM observations. It was revealed that the inclusion of nanoclay up to an appropriate level of content resulted in a remarkable enhancement in the thermal, mechanical (tensile strength/modulus), optical, and barrier properties of the prepared EVOH/clay nanocomposite films. However, excess clay loadings gave rise to a reduction in the tensile properties (strength/modulus/elongation) and optical transparency due to the formation of clay tactoids with a larger domain size. With the addition of only 3 wt % clay, the oxygen and water vapor barrier performances of the nanocomposite films were substantially improved by 59 and 90%, respectively, compared to the performances of the neat EVOH film. In addition, the presence of clay nanosheets in the EVOH matrix was found to significantly suppress the moisture‐derived deterioration in the oxygen barrier performance, implying the feasibility of applying the nanocomposite films to single‐layer food packaging films. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40289.
Dual band Trapezoidal antenna with Partial Ground and Meander line feed for GPS and WiMAX applications
Authors: Boney Macmillan , Rahim Sharul Kamal Abdul , Dewan Raimi , Sa'ad Bashir Muhammad 
Published: December 2013

ABSTRACTA dual band Trapezoidal antenna with Partial Ground and Meander line feed is proposed in this article. The antenna designed operates at 1.42–1.62 and 3.49–3.73 GHz simultaneously, which makes it suitable for 1.5 GHz global positioning system (GPS) and 3.5 GHz worldwide interoperability for microwave access (WiMAX) frequency bands, respectively. The antenna is fabricated on low‐cost FR‐4 substrate with 1.6 mm thickness. The proposed antenna consists of a trapezoidal‐shaped patch and a partial ground etched on bottom side of the strip. The antenna is fed through a meandered transmission line which reduces the overall antenna size. Moreover, the partial ground plane used facilitated the antenna radiation pattern to omnidirectional. The antenna is measured to observe the performance in comparison with simulated result. Gains of 1.7 and 3.4 dBi are recorded, with high gain especially at the second frequency band of the design. There is very good agreement between the simulation and measurement results. Hence, the antenna is suitable for GPS and WiMAX band applications. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:497–502, 2014
Bandwidth‐enhancement of an ultrathin polarization insensitive metamaterial absorber
Authors: Ghosh Saptarshi , Bhattacharyya Somak , Srivastava Kumar Vaibhav 
Published: December 2013

ABSTRACTAn ultrathin polarization insensitive microwave metamaterial absorber is discussed, which consists of a periodic array of swastika‐like structure printed on FR4 dielectric substrate backed by copper ground. The structure is simulated to give rise to nearly unity (99.64%) absorption at 10.10 GHz (X‐band). The proposed structure is symmetric in nature and provides high absorption for any angle of polarization under normal incidence. It also shows high absorption (∼81%) for incident angle upto 60o. Further, a 2 × 2 array using two different variants of the same resonating structure has been studied and by optimizing its geometrical dimensions, the absorption peaks are brought closer to provide an enhanced bandwidth having full width at half maximum of 0.68 GHz (10.04–10.72 GHz). Both the single‐band and bandwidth‐enhanced structures are then fabricated and experimentally studied which shows good agreement with the simulated results. © 2014 Wiley Periodicals, Inc. Microwave Opt Technol Lett 56:350–355, 2014
Synthesis and characterization of greenish‐blue emitting vinyl copolymer containing pyrene and triarylamine moieties
Authors: Wang Jianli , Leung Louis M , SO Shu‐Kong , Chan Cyrus Y H , Wong Michael Y 
Published: December 2013

AbstractTwo fluorescent monomers N‐phenyl‐N‐(4‐vinylphenyl)pyren‐1‐amine (vinyl‐PyPA) and 1‐vinyl pyrene (VPy) were synthesized in good yields. A series of soluble conductive vinyl copolymers P(PyPA‐co‐VPy) containing vinyl‐PyPA and VPy moieties in different composition ratios were prepared by free radical solution polymerization. These copolymers showed high Tg (190−201 °C) and good thermal stability. The photoluminescence emission maxima of the copolymers were all in the range 474.5−478.5 nm, which was similar to the poly(N‐phenyl‐N‐(4‐vinylphenyl)pyren‐1‐amine) (P(PyPA)) (475 nm) but blue shifted compared with poly(1‐vinyl pyrene) (PVPy) (490.5 nm). The lifetime of the copolymers increased from 10.2 to 29.7 ns with an increase in pyrene content. The copolymers had higher quantum yields (0.51) than those of the homopolymers of P(PyPA) (0.48) and PVPy (0.13). The highest occupied molecular orbital of the copolymers remained relatively unchanged from P(PyPA), while the lowest unoccupied molecular orbital varied from −2.41 eV to −2.51 eV with an increase in pyrene ratio in the copolymers. The energy bandgaps of the copolymers (from 2.70 eV to 2.81 eV) were smaller than those of P(PyPA) (2.82 eV) and PVPy (3.47 eV). Two polymer light‐emitting diode (PLED) series were attempted including indium tin oxide (ITO) (fluorocarbon (CFx) treated)/P(PyPA‐co‐VPy)/LiF/Al and ITO(CFx treated)/P(PyPA‐co‐VPy)/1,3,5‐Tri(1‐phenyl‐1H‐benzo[d]imidazol‐2‐yl)phenyl (TPBi)/LiF/Al. The results suggested that the PyPA moiety is hole conducting and the PLEDs can achieve high luminance from 650 to 1150 cd m−2 (at 100 mA cm−2) only when an electron injecting layer TPBi is employed. © 2013 Society of Chemical Industry
A formal framework for service modeling and prototyping
Authors: Riccobene Elvinia , Scandurra Patrizia 
Published: December 2013

Abstract

Service-oriented Computing
is rapidly gaining importance across several application domains due to its capability of composing autonomous and loosely-coupled services. In order to support the engineering of service-oriented software applications, foundational theories, service modeling notations, evaluation techniques fully integrated in a pragmatic software engineering approach are required. This article introduces a framework for modeling and prototyping service-oriented applications. The framework consists of a precise and executable language,
SCA-ASM
, for model-based design, and of a tool for early and quick design evaluation of service assemblies. The language combines the OASIS/OSOA standard
Service Component Architecture
(SCA) capability of modeling and assembling heterogeneous service-oriented components in a technology agnostic way, with the rigor of the
Abstract State Machine
(ASM) formal method able to model notions of service behavior, interactions, orchestration, compensation and context-awareness in an abstract but executable way. The tool is based on existing execution environments for ASM models and SCA applications. An SCA-ASM model of a service-oriented component, possibly not yet implemented in code or available as off-the-shelf, can be (i) simulated and evaluated
offline
, i.e. in isolation from the other components; or (ii) executed as
abstract implementation
(or
prototype
) together with the other components implementations according to the chosen SCA assembly. As proof of concept, a case study taken from EU research projects has been considered to show the functionalities and potentialities of the proposed framework.
Expression of 19 microRNAs in glioblastoma and comparison with other brain neoplasia of grades I–III
Authors: Visani Michela , de Biase Dario , Marucci Gianluca , Cerasoli Serenella , Nigrisoli Evandro , Bacchi Reggiani Maria Letizia , Albani Fiorenzo , Baruzzi Agostino , Pession Annalisa ,   the PERNO study group
Published: December 2013

Several biomarkers have been proposed as useful parameters to better specify the prognosis or to delineate new target therapy strategies for glioblastoma patients. MicroRNAs could represent putative target molecules, considering their role in tumorigenesis, cancer progression and their specific tissue expression. Although several studies have tried to identify microRNA signature for glioblastoma, a microRNA profile is still far from being well‐defined.In this work the expression of 19 microRNAs (miR‐7, miR‐9, miR‐9∗, miR‐10a, miR‐10b, miR‐17, miR‐20a, miR‐21, miR‐26a, miR‐27a, miR‐31, miR‐34a, miR‐101, miR‐137, miR‐182, miR‐221, miR‐222, miR‐330, miR‐519d) was evaluated in sixty formalin‐fixed and paraffin‐embedded glioblastoma samples using a locked nucleic acid real‐time PCR. Moreover, a comparison of miRNA expressions was performed between primary brain neoplasias of different grades (grades IV–I).The analysis of 14 validated miRNA expression in the 60 glioblastomas, using three different non‐neoplastic references as controls, revealed a putative miRNA signature: mir‐10b and miR‐21 were up‐regulated, while miR‐7, miR‐31, miR‐101, miR‐137, miR‐222 and miR‐330 were down‐regulated in glioblastomas. Comparing miRNA expression between glioblastoma group and gliomas of grades I–III, 3 miRNAs (miR‐10b, mir‐34a and miR‐101) showed different regulation statuses between high‐grade and low‐grade tumors. miR‐10b was up‐regulated in high grade and significantly down‐regulated in low‐grade gliomas, suggesting that could be a candidate for a GBM target therapy.This study provides further data for the identification of a miRNA profile for glioblastoma and suggests that different‐grade neoplasia could be characterized by different expression of specific miRNAs.