bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions
Authors: Skinner Michael K , Manikkam Mohan , Haque Md M , Zhang Bin , Savenkova Marina I 
Published: October 2012

Abstract
Background
Environmentally induced epigenetic transgenerational inheritance of adult onset disease involvesa variety of phenotypic changes, suggesting a general alteration in genome activity.

Results
Investigation of different tissue transcriptomes in male and female F3 generation vinclozolinversus control lineage rats demonstrated all tissues examined had transgenerational transcriptomes.The microarrays from 11 different tissues were compared with a gene bionetwork analysis. Althougheach tissue transgenerational transcriptome was unique, common cellular pathways and processes wereidentified between the tissues. A cluster analysis identified gene modules with coordinated geneexpression and each had unique gene networks regulating tissue-specific gene expression andfunction. A large number of statistically significant over-represented clusters of genes wereidentified in the genome for both males and females. These gene clusters ranged from 2-5 megabasesin size, and a number of them corresponded to the epimutations previously identified in sperm thattransmit the epigenetic transgenerational inheritance of disease phenotypes.

Conclusions
Combined observations demonstrate that all tissues derived from the epigenetically altered germline develop transgenerational transcriptomes unique to the tissue, but common epigenetic controlregions in the genome may coordinately regulate these tissue-specific transcriptomes. This systemsbiology approach provides insight into the molecular mechanisms involved in the epigenetictransgenerational inheritance of a variety of adult onset disease phenotypes.
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling
Authors: Boyle Patrick , Clement Kendell , Gu Hongcang , Smith Zachary D , Ziller Michael , Fostel Jennifer L , Holmes Laurie , Meldrim Jim , Kelley Fontina , Gnirke Andreas , Meissner Alexander 
Published: October 2012

AbstractSequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To further facilitate the mapping of DNA methylation, we describe a protocol for gel-free multiplexed reduced representation bisulfite sequencing (mRRBS) that reduces the workload dramatically and enables processing of 96 or more samples per week. mRRBS achieves similar CpG coverage to the original RRBS protocol, while the higher throughput and lower cost make it better suited for large-scale DNA methylation mapping studies, including cohorts of cancer samples.
Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome
Authors: Thomson John P , Lempiäinen Harri , Hackett Jamie A , Nestor Colm E , Müller Arne , Bolognani Federico , Oakeley Edward J , Schübeler Dirk , Terranova Rémi , Reinhardt Diana , Moggs Jonathan G , Meehan Richard R 
Published: October 2012

Abstract
Background
Induction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dynamics of 5-hydroxymethylcytosine (5hmC) as a likely intermediate of 5-methylcytosine (5mC) demethylation in a DNA methylation reprogramming pathway. We use a rodent model of non-genotoxic carcinogen exposure using the drug phenobarbital.

Results
Exposure to phenobarbital results in dynamic and reciprocal changes to the 5mC/5hmC patterns over the promoter regions of a cohort of genes that are transcriptionally upregulated. This reprogramming of 5mC/5hmC coincides with characteristic changes in the histone marks H3K4me2, H3K27me3 and H3K36me3. Quantitative analysis of phenobarbital-induced genes that are involved in xenobiotic metabolism reveals that both DNA modifications are lost at the transcription start site, while there is a reciprocal relationship between increasing levels of 5hmC and loss of 5mC at regions immediately adjacent to core promoters.

Conclusions
Collectively, these experiments support the hypothesis that 5hmC is a potential intermediate in a demethylation pathway and reveal precise perturbations of the mouse liver DNA methylome and hydroxymethylome upon exposure to a rodent hepatocarcinogen.
Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis
Authors: Berke Lidija , Sanchez-Perez Gabino F , Snel Berend 
Published: October 2012

Abstract
Background
Following gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns. The extent of divergence is influenced by several factors, including protein function. We examine whether an epigenetic modification, trimethylation of histone H3 at lysine 27 (H3K27me3), could be a factor in the evolution of expression patterns after gene duplication. Whereas in animals this repressive mark for transcription is deposited on long regions of DNA, in plants its localization is gene-specific. Because of this and a well-annotated recent whole-genome duplication, Arabidopsis thaliana is uniquely suited for studying the potential association of H3K27me3 with the evolutionary fate of genes.

Results
Paralogous pairs with H3K27me3 show the highest coding sequence divergence, which can be explained by their low expression levels. Interestingly, they also show the highest similarity in expression patterns and upstream regulatory regions, while paralogous pairs where only one gene is an H3K27me3 target show the highest divergence in expression patterns and upstream regulatory sequence. These trends in divergence of expression and upstream regions are especially pronounced for transcription factors.

Conclusions
After duplication, a histone modification can be associated with a particular fate of paralogs: H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence. Our results show that H3K27me3 constrains expression divergence after duplication. Moreover, its association with higher conservation of upstream regions provides a potential mechanism for the conserved H3K27me3 targeting of the paralogs.
Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers
Authors: Decock Anneleen , Ongenaert Maté , Hoebeeck Jasmien , De Preter Katleen , Van Peer Gert , Van Criekinge Wim , Ladenstein Ruth , Schulte Johannes H , Noguera Rosa , Stallings Raymond L , Van Damme An , Laureys Geneviève , Vermeulen Joëlle , Van Maerken Tom , Speleman Frank , Vandesompele Jo 
Published: October 2012

Abstract
Background
Accurate outcome prediction in neuroblastoma, which is necessary to enable the optimal choice of risk-related therapy, remains a challenge. To improve neuroblastoma patient stratification, this study aimed to identify prognostic tumor DNA methylation biomarkers.

Results
To identify genes silenced by promoter methylation, we first applied two independent genome-wide methylation screening methodologies to eight neuroblastoma cell lines. Specifically, we used re-expression profiling upon 5-aza-2'-deoxycytidine (DAC) treatment and massively parallel sequencing after capturing with a methyl-CpG-binding domain (MBD-seq). Putative methylation markers were selected from DAC-upregulated genes through a literature search and an upfront methylation-specific PCR on 20 primary neuroblastoma tumors, as well as through MBD- seq in combination with publicly available neuroblastoma tumor gene expression data. This yielded 43 candidate biomarkers that were subsequently tested by high-throughput methylation-specific PCR on an independent cohort of 89 primary neuroblastoma tumors that had been selected for risk classification and survival. Based on this analysis, methylation of KRT19, FAS, PRPH, CNR1, QPCT, HIST1H3C, ACSS3 and GRB10 was found to be associated with at least one of the classical risk factors, namely age, stage or MYCN status. Importantly, HIST1H3C and GNAS methylation was associated with overall and/or event-free survival.

Conclusions
This study combines two genome-wide methylation discovery methodologies and is the most extensive validation study in neuroblastoma performed thus far. We identified several novel prognostic DNA methylation markers and provide a basis for the development of a DNA methylation-based prognostic classifier in neuroblastoma.
Conductivity of Graphene-Like Thin Films Prepared from Chemically Exfoliated Carbon Nanotubes (CNTs), Highly Oriented Pyrolytic Graphite (HOPG), Natural Flake Graphite, and Carbon Powder
Authors: Marchese Matthew M. , Gerhardt Rosario A. 
Published: October 2012

ABSTRACTThe use of super acids such as chlorosulfonic acid (CSA) has proven to be extremely effective at exfoliating different forms of graphite in high concentrations without covalently functionalizing the surface of the graphene. Once quenched, the acid solutions can then be vacuum filtered through acid resistant polypropylene filter paper with an average pore size of 0.2 μm to collect the exfoliated carbon into a free standing retentate film. These films can then be easily washed, removed, and redispersed into solution by sonicating the films in a surfactant solution. Films were deposited onto various substrates using a range of spin coating parameters. This study has found that exfoliated CNTs provide the best conductivity out of the four types of chemically exfoliated carbon structures studied. CNTs have also proven to be the easiest type of exfoliated carbon to disperse and are able to stay in solution with less than 1%wt surfactant. The findings have shown that the electrical conductivity of the spin coated films actually increases with RPM and is inversely proportional to the film thickness. It is possible to achieve electrical conductivities as high as 10,507 ± 3728.64 [S/m] while still maintaining the transparency of the thin films. The initial spin coating step is more efficient at low ramp rates around 100 rpm/s and results in very smooth films. High spin speeds of 1800 rpm during the casting stage are found to play a large role in improving the conductivity of the films. Lastly, drying the samples on a hot plate for 5 min. on high has significantly improved the films electrical properties and virtually eliminated the need for tedious and expensive plasma cleaning treatments.
Rare-earth Activated Glass and Glass-Ceramic for Neutron Detection
Authors: Dai Wei , Marcacci Henry , Lynch Brendan , Menkara Hisham , Wagner Brent , Kang Zhitao , Wang Cai-Lin , Diawara Yacouba , Engels Ralf 
Published: October 2012

ABSTRACTNeutron detection scintillators based on rare-earth activated transparent glass and glass-ceramics are reported. Ce3+ doped gadolinium halides in 6LiF modified aluminosilicate glass matrices were synthesized by a melt-quench method followed by annealing. Their optical properties and alpha, neutron scintillation performance were investigated and compared to conventional 6Li-based scintillating glass.
Locating Closed Perforation Zones and Damaged Sections Using Well Test Analysis
Authors: Al Rbeawi S , Tiab D. 
Published: October 2012

Abstract
Closed perforations and damaged sections are two great challenges in the petroleum industry. Several reasons may cause these problems. Few of them depend on the type of formation and wellbore while others come from drilling, completion and stimulation activates before production process. Production rate and pressure drop may lead significantly to these two problems; therefore, production management sometimes plays great role in controlling them. Millions of dollars are spent annually for the remedial process of these two problems. Therefore the prediction of them is considered of great importance as an attempt to control them or reduce their negative impact on wellbore deliverability.
This paper introduces a new technique to predict closed perforations and damaged sections problems using pressure transient analysis. Pressure behaviors and flow regimes in the vicinity of horizontal wellbores are affected by the existence of the closed perforated zones and the formation sections where the resistance to reservoir fluid flow toward the wellbore is maximized. This resistance occurs because of the damaged permeability and high skin factor. Analytical models for predicting these problems and determining how many zones of the horizontal well that are considerably affected by them have been introduced in this study. These models have been derived based on the assumption that wellbore can be divided into multi-subsequent segments of producing and non-producing intervals. Producing intervals represent free flowing zones where there is no problem and both formation and wellbore are assumed to be clean. Non-producing intervals represent zones where both formation and wellbore’s perforations are closed or damaged.
The effective length of horizontal well where the perforated zones and the formation sections can not be considered problematic and the damaged length where both of them are significantly closed and damaged can be calculated. The numbers of the damaged zones can be calculated also. In addition, the locations of the damaged sections or closed perforated zones can be determined. Type-curve matching technique and the analytical models can be used for this purpose.
Analysis of Production Performance of the Hydraulically Fractured Horizontal Wells
Authors: Belyadi F. , Mashayekhi A. , Aminian K. , Ameri S. 
Published: October 2012

Abstract
The emergence of the ultra-low permeability formations, such as Marcellus Shale, as a target of exploration and development has created new challenges for resource development. To achieve economic production from shale formations massive stimulation treatments are required. Horizontal wells are the most effective in providing access to the formation to perform multi-stage hydraulic fracturing treatments. The limited field experience with multiple hydraulic fractures in horizontal wells indicates that significant increase in initial production can be achieved as the number of hydraulic fractures is increased. However, the production performance, particularly over longer time periods, is not well established.
The objective of this study was to analyze the production performance of multiply fractured horizontal well completed in Marcellus Shale to determine the long term production performance. The production history from a number of Marcellus Shale horizontal well in West Virginia were collected and analyzed using different commercial reservoir simulators. The impact of reservoir and hydraulic fracture parameters on the production performance and gas desorption were also investigated. The results indicated the presence of number of different flow regimes. The hydraulic fractures appear to dominate the early production performance while the later production is influenced by natural fractures. The results can be utilized to investigate the feasibility horizontal wells with multiple hydraulic fractures and optimize the production from the shale formation.
In vivo microcomputed tomography evaluation of rat alveolar bone and root resorption during orthodontic tooth movement
Authors: Ru Nan , Liu Sean Shih-Yao , Zhuang Li , Li Song , Bai Yuxing 
Published: October 2012

ABSTRACT

Objective:
To observe the real-time microarchitecture changes of the alveolar bone and root resorption during orthodontic treatment.

Materials and Methods:
A 10 g force was delivered to move the maxillary left first molars mesially in twenty 10-week-old rats for 14 days. The first molar and adjacent alveolar bone were scanned using in vivo microcomputed tomography at the following time points: days 0, 3, 7, and 14. Microarchitecture parameters, including bone volume fraction, structure model index, trabecular thickness, trabecular number, and trabecular separation of alveolar bone, were measured on the compression and tension side. The total root volume was measured, and the resorption crater volume at each time point was calculated. Univariate repeated measures analysis of variance with Bonferroni corrections were performed to compare the differences in each parameter between time points with significance level at P &lt; .05.

Results:
From day 3 to day 7, bone volume fraction, structure model index, trabecular thickness, and trabecular separation decreased significantly on the compression side, but the same parameters increased significantly on the tension side from day 7 to day 14. Root resorption volume of the mesial root increased significantly on day 7 of orthodontic loading.

Conclusions:
Real-time root and bone resorption during orthodontic movement can be observed in 3 dimensions using in vivo micro-CT. Alveolar bone resorption and root resorption were observed mostly in the apical third on day 7 on the compression side; bone formation was observed on day 14 on the tension side during orthodontic tooth movement.
Prevalence of Intestinal Parasitosis Among School Children in Baglung District of Western Nepal
Authors: Shrestha A , Narayan KC , Sharma R 
Published: October 2012

Background This study was carried out to estimate the prevalence of intestinal parasites among school-going children of the Baglung municipality from December 2010 to January 2011. Objective To find out prevalence of parasitosis among school aged children and to make necessary recommendations for preventive measures. Method A total of 260 stool samples were collected. A structured questionnaire was used to collect data on predisposing factors. Nails were observed without prior information to the subjects so as to find their hygienic practice. The stool samples were examined by direct wet mount and formal ether concentration technique. Results The total prevalence of the intestinal parasitosis was found to be 21.05%. The prevalence for individual parasites was as follows: Entamoeba histolytica (9.23%), Giardia lamblia (5.76%), Trichuris trichuria (5%), Ancylostoma duodenale (2.65%) and Ascaris lumbricoides (2.3%). Nail hygiene and level of education were significantly associated with intestinal parasitosis. The gender and age of the children, sanitary habits including toilet use, hand washing practice, and the use of the antihelminthic drug (albendazole) were not significantly associated with intestinal parasitosis. Higher prevalence was seen in boys, children belonging to age group 10-14 years, lower secondary students, among those who reported gastrointestinal problems within last six months, children from agriculture-based families and children with untrimmed nail. Conclusion Major contributors for the prevalence of parasites were found to be poor personal hygiene and educational level of the children. Health education and mass treatment are recommended as a preventive measures. KATHMANDU UNIVERSITY MEDICAL JOURNAL VOL.10 | NO. 1 | ISSUE 37 | JAN - MAR 2012 | 3-6 DOI: http://dx.doi.org/10.3126/kumj.v10i1.6904
Stigma Related to Tuberculosis Among Patients Attending DOTS Clinics of Dharan Municipality
Authors: Aryal S , Badhu A , Pandey S , Bhandari A , Khatiwoda P , Khatiwada P , Giri A 
Published: October 2012

Background The patients suffering from tuberculosis are receiving shame and unfair treatment from the people living around them within their own society attending DOTS clinic of Dharan municipality. Objective To assess the stigma experienced by tuberculosis patients and to find out the association between stigma experienced by Tuberculosis patient and the selected variables (socio-demographic characteristics, clinical profile and illness experience). Methods Descriptive Cross Sectional study was done among sixty tuberculosis patients. Stratified random sampling was used to select the main center and sub center of Tuberculosis treatment and population proportionate simple random sampling using lottery method was done. Data was collected using predesigned, pretested performa from Explanatory Model Interview Catalogue developed by World Health Organization. Results The study revealed that 63.3% of the subjects were stigmatized. There was association between stigma and variables such as occupation, monthly family income and past history of Tuberculosis. There was also association of stigma with treatment phase, category of the patient and past outcome of illness. Conclusion Due to lack of knowledge and awareness about Tuberculosis, many patients were stigmatized. Efforts should be made to educate the public about Tuberculosis to reduce stigma experienced by Tuberculosis patients and improve the compliance of the patient. KATHMANDU UNIVERSITY MEDICAL JOURNAL VOL.10 | NO. 1 | ISSUE 37 | JAN - MAR 2012 | 48-52 DOI: http://dx.doi.org/10.3126/kumj.v10i1.6914
Adenomyosis at Hysterectomy: Prevalence, Patient Characteristics, Clinical Profile and Histopatholgical Findings
Authors: Shrestha A , Shrestha R , Sedhai LB , Pandit U 
Published: October 2012

Background Underlying adenomyosis is often the cause of treatment failure for patients undergoing medical therapy for abnormal uterine bleeding and or chronic pelvic pain. Given the limitation of ultrasonography in diagnosing adenomyosis and MRI being unaffordable to most of the patients belonging to developing countries like us, it often remains undiagnosed before a hysterectomy. Objective To find out the clinical profile associated with adenomyosis and to determine the prevalence of adenomyosis in hysterectomy specimens; frequency distribution, as well as to correlate clinical examination with histopathological examination. Methods A total of 60 women who had undergone hysterectomy with histopathologically proven adenomyosis between April 2009 and March 2010 were included . Data were collected on indication for the intervention, age, symptoms, clinical findings, hemoglobin, menopausal status, gross and histopathological findings. Results A total of 256 women were scheduled for hysterectomy. Adenomyosis was diagnosed in 60 of 256 cases (23.4%). Menorrhagia (91.2%), dysmenorrhoea (84.2%), lower abdominal pain (84.2%) beginning later in reproductive life (mean age- 45yrs) is the classic presentation. Adenomyosis was present in 10 of 61 patients (16.3%) with fibroids; 27 of 60 (45%) with abnormal uterine bleeding; 11 of 55 (20%) with prolapse; four of 35 (11.4%) with ovarian mass; five of 25 (20%) with chronic pelvic pain; three of four (75%) with endometriosis. Conclusion Women undergoing hysterectomy with diagnosis of adenomyosis have a distinct symptomatology. The choice of therapy in adenomyosis is hysterectomy for those women who have completed family and had failed medical therapy . KATHMANDU UNIVERSITY MEDICAL JOURNAL VOL.10 | NO. 1 | ISSUE 37 | JAN - MAR 2012 | 53-56 DOI: http://dx.doi.org/10.3126/kumj.v10i1.6915