bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silico identification and characterization of the ion transport specificity for P-type ATPases in the Mycobacterium tuberculosis complex
Authors: Novoa-Aponte Lorena , León-Torres Andrés , Patiño-Ruiz Miyer , Cuesta-Bernal Jenifer , Salazar Luz-Mary , Landsman David , Mariño-Ramírez Leonardo , Soto Carlos-Yesid 
Published: October 2012

Abstract

Background
P-type ATPases hydrolyze ATP and release energy that is used in the transport of ions against electrochemical gradients across plasma membranes, making these proteins essential for cell viability. Currently, the distribution and function of these ion transporters in mycobacteria are poorly understood.

Results
In this study, probabilistic profiles were constructed based on hidden Markov models to identify and classify P-type ATPases in the Mycobacterium tuberculosis complex (MTBC) according to the type of ion transported across the plasma membrane. Topology, hydrophobicity profiles and conserved motifs were analyzed to correlate amino acid sequences of P-type ATPases and ion transport specificity. Twelve candidate P-type ATPases annotated in the M. tuberculosis H37Rv proteome were identified in all members of the MTBC, and probabilistic profiles classified them into one of the following three groups: heavy metal cation transporters, alkaline and alkaline earth metal cation transporters, and the beta subunit of a prokaryotic potassium pump. Interestingly, counterparts of the non-catalytic beta subunits of Hydrogen/Potassium and Sodium/Potassium P-type ATPases were not found.

Conclusions
The high content of heavy metal transporters found in the MTBC suggests that they could play an important role in the ability of M. tuberculosis to survive inside macrophages, where tubercle bacilli face high levels of toxic metals. Finally, the results obtained in this work provide a starting point for experimental studies that may elucidate the ion specificity of the MTBC P-type ATPases and their role in mycobacterial infections.
Calcification of vestibular schwannoma: a case report and literature review
Authors: Zhang Yang , Yu Jinlu , Qu Limei , Li Yunqian 
Published: October 2012

Abstract
Calcification rarely occurs in vestibular schwannoma (VS), and only seven cases of calcified VS have been reported in the literature. Here, we report a 48-year-old man with VS, who had a history of progressive left-sided hearing loss for 3 years. Neurological examination revealed that he had left-sided hearing loss and left cerebellar ataxia. Magnetic resonance imaging and computerized tomography angiography showed a mass with calcification in the left cerebellopontine angle (CPA). The tumor was successfully removed via suboccipital craniotomy, and postoperative histopathology showed that the tumor was a schwannoma. We reviewed seven cases of calcified VS that were previously reported in the literature, and we analyzed and summarized the characteristics of these tumors, including the calcification, texture, and blood supply. We conclude that calcification in VS is associated with its texture and blood supply, and these characteristics affect the surgical removal of the tumor.
Synthesis route and three different core-shell impacts on magnetic characterization of gadolinium oxide-based nanoparticles as new contrast agents for molecular magnetic resonance imaging
Authors: Azizian Gholamreza , Riyahi-Alam Nader , Haghgoo Soheila , Moghimi Hamid Reza , Zohdiaghdam Reza , Rafiei Behrooz , Gorji Ensieh 
Published: October 2012

Abstract
Despite its good resolution, magnetic resonance imaging intrinsically has low sensitivity. Recently, contrast agent nanoparticles have been used as sensitivity and contrast enhancer. The aim of this study was to investigate a new controlled synthesis method for gadolinium oxide-based nanoparticle preparation. For this purpose, diethyleneglycol coating of gadolinium oxide (Gd2O3-DEG) was performed using new supervised polyol route, and small particulate gadolinium oxide (SPGO) PEGylation was obtained with methoxy-polyethylene-glycol-silane (550 and 2,000 Da) coatings as SPGO-mPEG-silane550 and 2,000, respectively. Physicochemical characterization and magnetic properties of these three contrast agents in comparison with conventional Gd-DTPA were verified by dynamic light scattering transmission electron microscopy, Fourier transform infrared spectroscopy, inductively coupled plasma, X-ray diffraction, vibrating sample magnetometer, and the signal intensity and relaxivity measurements were performed using 1.5-T MRI scanner.
As a result, the nanoparticle sizes of Gd2O3-DEG, SPGO-mPEG-silane550, and SPGO-mPEG-silane2000 could be reached to 5.9, 51.3, 194.2 nm, respectively. The image signal intensity and longitudinal (r
1) and transverse relaxivity (r
2) measurements in different concentrations (0.3 to approximately 2.5 mM), revealed the r
2/r
1 ratios of 1.13, 0.89, 33.34, and 33.72 for Gd-DTPA, Gd2O3-DEG, SPGO-mPEG-silane550, and SPGO-mPEG-silane2000, respectively.
The achievement of new synthesis route of Gd2O3-DEG resulted in lower r
2/r
1 ratio for Gd2O3-DEG than Gd-DTPA and other previous synthesized methods by this and other groups. The smaller r
2/r
1 ratios of two PEGylated-SPGO contrast agents in our study in comparison with r
2/r
1 ratio of previous PEGylation (r
2/r
1 = 81.9 for mPEG-silane 6,000 MW) showed that these new three introduced contrast agents could potentially be proper contrast enhancers for cellular and molecular MR imaging.
Coupled fixed point theorems for nonlinear contractions without mixed monotone property
Authors: Sintunavarat Wutiphol , Kumam Poom , Cho Yeol Je 
Published: October 2012

Abstract
In this paper, we show the existence of a coupled fixed point theorem of nonlinear contraction mappings in complete metric spaces without the mixed monotone property and give some examples of a nonlinear contraction mapping, which is not applied to the existence of coupled fixed point by using the mixed monotone property. We also study the necessary condition for the uniqueness of a coupled fixed point of the given mapping. Further, we apply our results to the existence of a coupled fixed point of the given mapping in partially ordered metric spaces. Moreover, some applications to integral equations are presented.

MSC:47H10, 54H25.
Generation and characterization of a recombinant Newcastle disease virus expressing the red fluorescent protein for use in co-infection studies
Authors: Li Jinnan , Hu Haixia , Yu Qingzhong , Diel Diego G , Li De-shan , Miller Patti J 
Published: October 2012

Abstract

Background
Many viruses have evolved multiple strategies to prevent super infection of host cells by more than one virion. This phenomenon, known as super infection exclusion, may play an important role on virus evolution because it can affect the frequency of reassortment and/or recombination. Newcastle disease virus (NDV), a negative sense single-stranded RNA virus, is characterized by its continuous evolutionary dynamics and by a low frequency of recombination events. However, the mechanisms that contribute to the low recombination rates on NDV are still not completely understood.

Methods
In this study we assessed the ability of two NDV strains (LaSota and B1) to super infect host cells in vitro. We generated a recombinant NDV strain LaSota expressing the red fluorescent protein (RFP) and used it in co-infection assays with a related NDV strain B1 expressing the green fluorescent protein (GFP). DF-1 cells were inoculated with both viruses at the same time or at different intervals between primary infection and super infection.

Results
When both viruses were inoculated at the same time point, a 27% co-infection rate was observed, whereas when they were inoculated at different time points the super infection rates decreased to levels as low as 1.4%.

Conclusions
These results indicate that although different NDV strains can co-infect host cells in vitro, the super infection rates are low, specially as the time between the primary infection and super infection increases. These results confirm the occurrence of super infection exclusion between different strains of NDV.
Neuroprotective properties of Melissa officinalis after hypoxic-ischemic injury both in vitro and in vivo
Authors: Bayat Mohammad , Azami Tameh Abolfazl , Hossein Ghahremani Mohammad , Akbari Mohammad , Mehr Shahram Ejtemaei , Khanavi Mahnaz , Hassanzadeh Gholamreza 
Published: October 2012

Abstract

Background
Brain ischemia initiates several metabolic events leading to neuronal death. These events mediate large amount of damage that arises after some neurodegenerative disorders as well as transient brain ischemia. Melissa officinalis is considered as a helpful herbal plant in the prevention of various neurological diseases like Alzheimer that is related with oxidative stress.

Methods
We examined the effect of Melissa officinalis on hypoxia induced neuronal death in a cortical neuronal culture system as in vitro model and transient hippocampal ischemia as in vivo model. Transient hippocampal ischemia was induced in male rats by tow vessel-occlusion for 20 min. After reperfusion, the histopathological changes and the levels inflammation, oxidative stress status, and caspase-3 activity in hippocampus were measured.

Results
Cytotoxicity assays showed a significant protection of a 10 μg/ml dose of Melissa against hypoxia in cultured neurons which was confirmed by a conventional staining (P<0.05). Melissa treatment decrease caspase3 activity (P<0.05) and TUNEL-positive cells significantly (P<0.01). Melissa oil has also inhibited malon dialdehyde level and attenuated decrease of Antioxidant Capacity in the hippocampus. Pro-inflammatory cytokines TNF-α, IL-1β and HIF-1α mRNA levels were highly increased after ischemia and treatment with Melissa significantly suppressed HIF-1α gene expression (P<0.05).

Discussion
Results showed that Melissa officinalis could be considered as a protective agent in various neurological diseases associated with ischemic brain injury.
Derivation of a pediatric growth curve for inferior vena caval diameter in healthy pediatric patients: brief report of initial curve development
Authors: Haines Elizabeth J , Chiricolo Gerardo C , Aralica Kresimir , Briggs William M , Van Amerongen Robert , Laudenbach Andrew , O’Rourke Kevin , Melniker Lawrence 
Published: October 2012

Abstract

Background
A validated tool has long been sought to provide clinicians with a uniform and accurate method to assess hydration status in the pediatric emergency medicine population. Outpatient clinicians use CDC height- and weight-based curves for the assessment of physical development. In hospital, daily weights provide objective data; however, these are usually not available at presentation.
One of the most promising techniques for the rapid assessment of volume is ultrasound (US) to obtain an indexed inferior vena cava diameter (IVCDi); as previously described. Prior studies have focused on IVCDi in dehydrated patients and have shown that it provides accurate estimates of right atrial pressure and volume status. The objective of this study is to derive an IVC growth curve in healthy pediatric patients.

Methods
Prospective cohort design enrolled healthy children between the ages of 4 weeks and 20 years. Patients presenting with fever, illnesses, or diagnoses known to affect the volume will be excluded. All eligible patients under 21, who have provided self or parental written consent, will undergo a brief ultrasound to obtain transverse and long images of both the IVC and the aorta; all scans will be digitally saved. Image quality will be subjectively rated as poor, fair, or good based on wall clarity. Poor quality images will be recorded but may be omitted from our analysis. Five clinicians completed a 1-h introduction to IVC-US and ten supervised scans prior to enrollment. Still images will be measured in order to determine IVCDi in both transverse and longitudinal planes. To assess inter-rater reliability, in 10% of cases, two clinicians will complete scans. All study scans will be over-read by a fellowship-trained sonologist.
IVCDi will be plotted independently as functions of age, gender, BMI, and aortic diameter. Within each group, means with means or medians with 95% CIs will be calculated. Following uni- and bivariate analyses and assessment for colinearity, a variety of parametric and nonparametric regression procedures will be conducted. The smoothed curves will be approximated using a modified LMS estimation procedure.

Results
Data for the initial curve derivation includes 25 patients ranging from 13 months to 20 years (mean 102 months or 8.5 years). Sixty-five percent of patients were enrolled from the ED, while 35% were enrolled from well-child clinic visits. When evaluating the size of IVC as a function of time linear growth, increasing size was found to proportionately increase with age of patient in months.

Conclusions
Data suggest a linear correlation between IVC size and age. Such data, when plotted as a new growth curve, may allow clinicians to plot a patient's sonographic measurements in order to assess hydration health.
Development and study of the structural and optical properties of hexagonal ZnO nanocrystals
Authors: Khan Ziaul Raza , Arif Mohd , Singh Arun 
Published: October 2012

AbstractZnO is a promising member of the semiconducting materials of II-VI group. ZnO nanocrystals have shown potential applications in various novel technologies. In the present investigation of ZnO nanocrystals, a novel chemical route using Zinc acetate as organic precursor is being reported. ZnO nanocrystals were characterized using X-ray diffraction, scanning electron microscopy UV-visible (UV–vis) spectroscopy, and photoluminescence measurements. The X-ray diffraction studies reveal the typical hexagonal structure of ZnO nanocrystals along the preferred orientation of (101) and (100) planes. The optical bandgap of ZnO nanocrystals was found to be 3.50 eV from the absorbance spectrum, which is higher than that of the bulk ZnO material. A blueshift of 21 nm is observed in the excitonic transitions, which clearly indicates the formation of ZnO nanocrystals. Photoluminescence spectroscopy of the ZnO nanocrystals showed a strong emission peak at 365 nm near the band edge along with a weak green-yellow emission peak spanning the range of 450 to 600 nm. The blueshifting was also observed in the photoluminescence spectrum, in accordance with the UV–vis spectroscopy in contrast to the bulk ZnO material.
Effect of non-clinical inter-hospital critical care unit to unit transfer of critically ill patients: a propensity-matched cohort analysis
Authors: Barratt Helen , Harrison David A , Rowan Kathryn M , Raine Rosalind 
Published: October 2012

Abstract
Introduction
No matter how well resourced, individual hospitals cannot expect to meet all peaks in demand for adult general critical care. However, previous analyses suggest that patients transferred for non-clinical reasons have worse outcomes than those who are not transferred, but these studies were underpowered and hampered by residual case-mix differences. The aim of this study was to evaluate the effect of transferring adult general critical care patients to other hospitals for non-clinical reasons.

Methods
We carried out a propensity-matched cohort analysis comparing critical care patients who underwent a non-clinical critical care unit to unit transfer to another hospital with those who were not transferred. The primary outcome measure was mortality at ultimate discharge from acute hospital. Secondary outcomes were mortality at ultimate discharge from critical care, plus length of stay in both critical care and acute hospital.

Results
A total of 308,323 patients were admitted to one of 198 adult general critical care units in England and Wales between January 2008 and September 2011. This included 759 patients who underwent a non-clinical transfer within 48 hours of admission to the unit and 1,518 propensity-matched patients who were not transferred. The relative risk of ultimate acute hospital mortality was 1.01 (95% confidence interval = 0.87 to 1.16) for the non-clinical transfer group, compared with patients who were not transferred but had a similar propensity for transfer. There was no statistically significant difference in ultimate critical care unit mortality. Transferred patients received on average three additional days of critical care (P < 0.001) but the difference in length of acute hospital stay was of only borderline significance (P = 0.05).

Conclusion
In our analysis the difference in mortality between non-clinical transferred and nontransferred patients was not statistically significant. Nevertheless, non-clinical transfers received, on average, an additional 3 days of critical care. This has potential ramifications in terms of distress, inconvenience and cost for patients, their families, and the National Health Service. We therefore need further evidence, including qualitative data from family members and cost-effective analyses, to better understand the broader effects of non-clinical transfer.
BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation
Authors: Lim Jing-Quan , Tennakoon Chandana , Li Guoliang , Wong Eleanor , Ruan Yijun , Wei Chia-Lin , Sung Wing-Kin 
Published: October 2012

AbstractDNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/.
Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns
Authors: Sproul Duncan , Kitchen Robert R , Nestor Colm E , Dixon J Michael , Sims Andrew H , Harrison David J , Ramsahoye Bernard H , Meehan Richard R 
Published: October 2012

Abstract
Background
Aberrant CpG island promoter DNA hypermethylation is frequently observed in cancer and is believed to contribute to tumor progression by silencing the expression of tumor suppressor genes. Previously, we observed that promoter hypermethylation in breast cancer reflects cell lineage rather than tumor progression and occurs at genes that are already repressed in a lineage-specific manner. To investigate the generality of our observation we analyzed the methylation profiles of 1,154 cancers from 7 different tissue types.

Results
We find that 1,009 genes are prone to hypermethylation in these 7 types of cancer. Nearly half of these genes varied in their susceptibility to hypermethylation between different cancer types. We show that the expression status of hypermethylation prone genes in the originator tissue determines their propensity to become hypermethylated in cancer; specifically, genes that are normally repressed in a tissue are prone to hypermethylation in cancers derived from that tissue. We also show that the promoter regions of hypermethylation-prone genes are depleted of repetitive elements and that DNA sequence around the same promoters is evolutionarily conserved. We propose that these two characteristics reflect tissue-specific gene promoter architecture regulating the expression of these hypermethylation prone genes in normal tissues.

Conclusions
As aberrantly hypermethylated genes are already repressed in pre-cancerous tissue, we suggest that their hypermethylation does not directly contribute to cancer development via silencing. Instead aberrant hypermethylation reflects developmental history and the perturbation of epigenetic mechanisms maintaining these repressed promoters in a hypomethylated state in normal cells.
Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity
Authors: Tewari Alok K , Yardimci Galip Gürkan , Shibata Yoichiro , Sheffield Nathan C , Song Lingyun , Taylor Barry S , Georgiev Stoyan G , Coetzee Gerhard A , Ohler Uwe , Furey Terrence S , Crawford Gregory E , Febbo Phillip G 
Published: October 2012

Abstract
Background
Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prostate cancer pathogenesis, acts primarily through ligand-activated transcription of target genes. Although several determinants of AR transcriptional specificity have been elucidated, our understanding of the interplay between chromatin accessibility and AR function remains incomplete.

Results
We used deep sequencing to assess chromatin structure via DNase I hypersensitivity and mRNA abundance, and paired these datasets with three independent AR ChIP-seq datasets. Our analysis revealed qualitative and quantitative differences in chromatin accessibility that corresponded to both AR binding and an enrichment of motifs for potential collaborating factors, one of which was identified as SP1. These quantitative differences were significantly associated with AR-regulated mRNA transcription across the genome. Base-pair resolution of the DNase I cleavage profile revealed three distinct footprinting patterns associated with the AR-DNA interaction, suggesting multiple modes of AR interaction with the genome.

Conclusions
In contrast with other DNA-binding factors, AR binding to the genome does not only target regions that are accessible to DNase I cleavage prior to hormone induction. AR binding is invariably associated with an increase in chromatin accessibility and, consequently, changes in gene expression. Furthermore, we present the first in vivo evidence that a significant fraction of AR binds only to half of the full AR DNA motif. These findings indicate a dynamic quantitative relationship between chromatin structure and AR-DNA binding that impacts AR transcriptional specificity.
The landscape of DNA repeat elements in human heart failure
Authors: Haider Syed , Cordeddu Lina , Robinson Emma , Movassagh Mehregan , Siggens Lee , Vujic Ana , Choy Mun-Kit , Goddard Martin , Lio Pietro , Foo Roger 
Published: October 2012

Abstract
Background
The epigenomes of healthy and diseased human hearts were recently examined by genome-wide DNA methylation profiling. Repetitive elements, heavily methylated in post-natal tissue, have variable methylation profiles in cancer but methylation of repetitive elements in the heart has never been examined.

Results
We analyzed repetitive elements from all repeat families in human myocardial samples, and found that satellite repeat elements were significantly hypomethylated in end-stage cardiomyopathic hearts relative to healthy normal controls. Satellite repeat elements are almost always centromeric or juxtacentromeric, and their overexpression correlates with disease aggressiveness in cancer. Similarly, we found that hypomethylation of satellite repeat elements correlated with up to 27-fold upregulation of the corresponding transcripts in end-stage cardiomyopathic hearts. No other repeat family exhibited differential methylation between healthy and cardiomyopathic hearts, with the exception of the Alu element SINE1/7SL, for which a modestly consistent trend of increased methylation was observed.

Conclusions
Satellite repeat element transcripts, a form of non-coding RNA, have putative functions in maintaining genomic stability and chromosomal integrity. Further studies will be needed to establish the functional significance of these non-coding RNAs in the context of heart failure.