bluuebunny/crossref_metadata_2025 huggingface dataset:
Processing Load Induced by Informational Masking Is Related to Linguistic Abilities
Authors: Koelewijn Thomas , Zekveld Adriana A. , Festen Joost M. , Rönnberg Jerker , Kramer Sophia E.
Published: October 2012

It is often assumed that the benefit of hearing aids is not primarily reflected in better speech performance, but that it is reflected in less effortful listening in the aided than in the unaided condition. Before being able to assess such a hearing aid benefit the present study examined how processing load while listening to masked speech relates to inter-individual differences in cognitive abilities relevant for language processing. Pupil dilation was measured in thirty-two normal hearing participants while listening to sentences masked by fluctuating noise or interfering speech at either 50% and 84% intelligibility. Additionally, working memory capacity, inhibition of irrelevant information, and written text reception was tested. Pupil responses were larger during interfering speech as compared to fluctuating noise. This effect was independent of intelligibility level. Regression analysis revealed that high working memory capacity, better inhibition, and better text reception were related to better speech reception thresholds. Apart from a positive relation to speech recognition, better inhibition and better text reception are also positively related to larger pupil dilation in the single-talker masker conditions. We conclude that better cognitive abilities not only relate to better speech perception, but also partly explain higher processing load in complex listening conditions.
Generation of a Chinese Hamster Ovary Cell Line Producing Recombinant Human Glucocerebrosidase
Authors: Novo Juliana Branco , Morganti Ligia , Moro Ana Maria , Paes Leme Adriana Franco , Serrano Solange Maria de Toledo , Raw Isaias , Ho Paulo Lee
Published: October 2012

Impaired activity of the lysosomal enzyme glucocerebrosidase (GCR) results in the inherited metabolic disorder known as Gaucher disease. Current treatment consists of enzyme replacement therapy by administration of exogenous GCR. Although effective, it is exceptionally expensive, and patients worldwide have a limited access to this medicine. In Brazil, the public healthcare system provides the drug free of charge for all Gaucher’s patients, which reaches the order of $ 84 million per year. However, the production of GCR by public institutions in Brazil would reduce significantly the therapy costs. Here, we describe a robust protocol for the generation of a cell line producing recombinant human GCR. The protein was expressed in CHO-DXB11 (dhfr−) cells after stable transfection and gene amplification with methotrexate. As expected, glycosylated GCR was detected by immunoblotting assay both as cell-associated (~64 and 59 kDa) and secreted (63–69 kDa) form. Analysis of subclones allowed the selection of stable CHO cells producing a secreted functional enzyme, with a calculated productivity of 5.14 pg/cell/day for the highest producer. Although being laborious, traditional methods of screening high-producing recombinant cells may represent a valuable alternative to generate expensive biopharmaceuticals in countries with limited resources.
Dermal Ultrastructure in Low Beighton Score Members of 17 Families with Hypermobile-Type Ehlers-Danlos Syndrome
Authors: Hermanns-Lê Trinh , Reginster Marie-Annick , Piérard-Franchimont Claudine , Delvenne Philippe , Piérard Gérald E. , Manicourt Daniel
Published: October 2012

The distinction between the Ehlers-Danlos syndrome hypermobile type (EDSH) and the benign joint hypermobility syndrome (BJHS) is unclear. The aim of the present study was to compare skin ultrastructural abnormalities of EDSH and BJHS among different families. Skin of 23 EDSH, 27 BJHS, and 41 asymptomatic subjects from 17 families was examined using transmission electron microscopy. Similar ultrastructural abnormalities were found irrespective of the Beighton score. Flower-like collagen fibrils represented the key change and elastic fibers were altered as well. Beighton score is a clinical parameter rating joint mobility that appeared unrelated to quantitative and qualitative collagen ultrastructural alterations in the skin. Some EDSH family members fit with BJHS diagnosis. BJHS possibly represents a mild variant of EDSH.
Hesperidin-3′-O-Methylether Is More Potent than Hesperidin in Phosphodiesterase Inhibition and Suppression of Ovalbumin-Induced Airway Hyperresponsiveness
Authors: Yang You-Lan , Hsu Hsin-Te , Wang Kuo-Hsien , Wang Chao-Sian , Chen Chien-Ming , Ko Wun-Chang
Published: October 2012

Hesperidin is present in the traditional Chinese medicine, “Chen Pi,” and recently was reported to have anti-inflammatory effects. Therefore, we were interested in comparing the effects of hesperidin and hesperidin-3′-O-methylether on phosphodiesterase inhibition and airway hyperresponsiveness (AHR) in a murine model of asthma. In the present results, hesperidin-3′-O-methylether, but not hesperidin, at 30 μmol/kg (p.o.) significantly attenuated the enhanced pause (Penh) value, suppressed the increases in numbers of total inflammatory cells, macrophages, lymphocytes, neutrophils, and eosinophils, suppressed total and OVA-specific immunoglobulin (Ig)E levels in the serum and BALF, and enhanced the level of totalIgG2ain the serum of sensitized and challenged mice, suggesting that hesperidin-3′-O-methylether is more potent than hesperidin in suppression of AHR and immunoregulation. The different potency between them may be due to their aglycons, because these two flavanone glycosides should be hydrolyzed byβ-glucosidase after oral administration. Neither influenced xylazine/ketamine-induced anesthesia, suggesting that they may have few or no adverse effects, such as nausea, vomiting, and gastric hypersecretion. In conclusion, hesperidin-3′-O-methylether is more potent in phosphodiesterase inhibition and suppression of AHR and has higher therapeutic (PDE4H/PDE4L) ratio than hesperidin. Thus, hesperidin-3′-O-methylether may have more potential for use in treating allergic asthma and chronic obstructive pulmonary disease.
Hydrogenation of Some Vegetable Oils by Scrap Automobile Catalyst
Authors: Sonmez Fatih , Ercan Hakan , Genc Hayriye , Arslan Mustafa , Zengin Mustafa , Kucukislamoglu Mustafa
Published: October 2012

Some vegetable oils were hydrogenated with scrap automobile catalyst (SAC) as a catalyst. The optimum reaction conditions (solvent, reaction time, and catalyst amount) were determined. Our results showed that the linoleic acid was reduced to elaidic acid in the sunflower oil. This procedure not only gives high yields but also allows recycling of automobile wastes as a catalyst in organic reactions and is representative of green chemistry.
Unexpected Dissemination Patterns in Lymphoma Progression Revealed by Serial Imaging within a Murine Lymph Node
Authors: Ito Ken , Smith Bryan Ronain , Parashurama Natesh , Yoon Joon-Kee , Song Si Yeol , Miething Cornelius , Mallick Parag , Lowe Scott , Gambhir Sanjiv Sam
Published: October 2012

Non-Hodgkin lymphoma (NHL) is a heterogeneous and highly disseminated disease, but the mechanisms of its growth and dissemination are not well understood. Using a mouse model of this disease, we used multimodal imaging, including intravital microscopy (IVM) combined with bioluminescence, as a powerful tool to better elucidate NHL progression. We injected enhanced green fluorescent protein and luciferase-expressing Eμ-Myc/Arf−/− (Cdkn2a−/−) mouse lymphoma cells (EL-Arf−/−) into C57BL/6NCrl mice intravenously. Long-term observation inside a peripheral lymph node was enabled by a novel lymph node internal window chamber technique that allows chronic, sequential lymph node imaging under in vivo physiologic conditions. Interestingly, during early stages of tumor progression we found that few if any lymphoma cells homed initially to the inguinal lymph node (ILN), despite clear evidence of lymphoma cells in the bone marrow and spleen. Unexpectedly, we detected a reproducible efflux of lymphoma cells from spleen and bone marrow, concomitant with a massive and synchronous influx of lymphoma cells into the ILN, several days after injection. We confirmed a coordinated efflux/influx of tumor cells by injecting EL-Arf−/− lymphoma cells directly into the spleen and observing a burst of lymphoma cells, validating that the burst originated in organs remote from the lymph nodes. Our findings argue that in NHL an efflux of tumor cells from one disease site to another, distant site in which they become established occurs in discrete bursts. Cancer Res; 72(23); 6111–8. ©2012 AACR.
Establishment and Characterization of Novel Cell Lines from Sinonasal Undifferentiated Carcinoma
Authors: Takahashi Yoko , Kupferman Michael E. , Bell Diana , Jiffar Tilahun , Lee June Goo , Xie Tong-Xin , Li Ning-Wei , Zhao Mei , Frederick Mitchell J. , Gelbard Alexander , Myers Jeffrey N. , Hanna Ehab Y.
Published: October 2012

Purpose: Sinonasal undifferentiated carcinoma (SNUC) is a rare and aggressive cancer. Despite the use of multimodality treatment, the overall prognosis remains poor. To better understand the biologic features of SNUC and help develop new therapies for the disease, we established SNUC cell lines and characterized their biologic behaviors.

Experimental Design: Cell lines were established from a patient with a T4N0M0 SNUC of the right maxillary sinus who was treated with surgical resection at our center. Tumor colonies were harvested and were sequentially replated onto larger plates. Two populations were developed and labeled MDA8788-6 and MDA8788-7. These cell lines were characterized with molecular, biomarker, functional, and histologic analyses.

Results: Short tandem repeat genotyping revealed that the cell line is isogenic to the parental tumor, and cytogenetic analysis identified 12 chromosomal translocations. The SNUC cell lines do not form colonies in soft agar but are tumorigenic and nonmetastatic in an orthotopic mouse model of sinonasal cancer. Western blot analysis revealed that both MDA8788 cell lines express epithelial markers but do not express mesenchymal markers or the endocrine marker synaptophysin.

Conclusions: This is the first report of the establishment of stable human-derived SNUC cell lines. The lines were highly tumorigenic and maintain the histologic and molecular features of the original tumor. These cell lines should serve as useful tools for the future study of SNUC biology and the development and testing of novel therapies for this deadly disease. Clin Cancer Res; 18(22); 6178–87. ©2012 AACR.
Phase I Trial of Overlapping Long Peptides from a Tumor Self-Antigen and Poly-ICLC Shows Rapid Induction of Integrated Immune Response in Ovarian Cancer Patients
Authors: Sabbatini Paul , Tsuji Takemasa , Ferran Luis , Ritter Erika , Sedrak Christine , Tuballes Kevin , Jungbluth Achim A. , Ritter Gerd , Aghajanian Carol , Bell-McGuinn Katherine , Hensley Martee L. , Konner Jason , Tew William , Spriggs David R. , Hoffman Eric W. , Venhaus Ralph , Pan Linda , Salazar Andres M. , Diefenbach Catherine Magid , Old Lloyd J. , Gnjatic Sacha
Published: October 2012

Purpose: Long peptides are efficiently presented to both CD4+ and CD8+ T cells after intracellular processing by antigen-presenting cells. To investigate the safety and in vivo immunogenicity of synthetic overlapping long peptides (OLP) from a human tumor self-antigen, we conducted a phase I clinical trial with OLP from cancer-testis antigen NY-ESO-1 in various adjuvant combinations.

Experimental Design: Twenty-eight patients with advanced ovarian cancer in second or third remission were enrolled sequentially in three cohorts and received at least one vaccination. Patients in Cohort 1 (n = 4) received 1.0 mg OLP, Cohort 2 (n = 13) received OLP in Montanide-ISA-51, and Cohort 3 (n = 11) received OLP + 1.4 mg Poly-ICLC in Montanide-ISA-51 on weeks 1, 4, 7, 10, and 13. Humoral and cellular responses were evaluated by standardized immunomonitoring techniques (ELISA, ELISPOT assay, intracellular cytokine staining, and tetramer staining).

Results: The vaccine was generally well tolerated with injection site reactions and fatigue that resolved. NY-ESO-1–specific antibody and CD8+ T cells were undetectable after vaccination with OLP alone, but were found in 6 of 13 (46%) and 8 of 13 (62%) patients, respectively, after vaccination with OLP+Montanide, and in 10 of 11 (91%) and 10 of 11 (91%) patients, respectively, after vaccination with OLP+Montanide+Poly-ICLC. NY-ESO-1–specific CD4+ T cells were detected in all patients with greater frequency and polyclonality when Montanide-ISA-51 was used for vaccination. Inclusion of Poly-ICLC as an adjuvant further accelerated the induction of NY-ESO-1–specific immune responses.

Conclusions: The current study shows that NY-ESO-1 OLP vaccine is safe and rapidly induces consistent integrated immune responses (antibody, CD8+ and CD4+) in nearly all vaccinated patients when given with appropriate adjuvants. Clin Cancer Res; 18(23); 6497–508. ©2012 AACR.
Acute Heart Failure
Authors: Ezekowitz Justin A. , Hu Jia , Delgado Diego , Hernandez Adrian F. , Kaul Padma , Leader Rolland , Proulx Guy , Virani Sean , White Michel , Zieroth Shelley , O’Connor Christopher , Westerhout Cynthia M. , Armstrong Paul W.
Published: October 2012

Background—

Randomized controlled trials (RCT) are limited by their generalizability to the broader nontrial population. To provide a context for Acute Study of Nesiritide in Decompensated Heart Failure (ASCEND-HF) trial, we designed a complementary registry to characterize clinical characteristics, practice patterns, and in-hospital outcomes of acute heart failure patients.

Methods and Results—

Eligible patients for the registry included those with a principal diagnosis of acute heart failure (ICD-9-CM 402 and 428; ICD-10 I50.x, I11.0, I13.0, I13.2) from 8 sites participating in ASCEND-HF (n=697 patients, 2007–2010). Baseline characteristics, treatments, and hospital outcomes from the registy were compared with ASCEND-HF RCT patients from 31 Canadian sites (n=465, 2007–2010). Patients in the registry were older, more likely to be female, and have chronic respiratory disease, less likely to have diabetes mellitus: they had a similar incidence of ischemic HF, atrial fibrillation, and similar B-type natriuretic peptide levels. Registry patients had higher systolic blood pressure (registry: median 132 mm Hg [interquartile range 115–151 mm Hg]; RCT: median 120 mm Hg [interquartile range 110–135 mm Hg]) and ejection fraction (registry: median 40% [interquartile range 27–58%]; RCT: median 29% [interquartile range 20–40 mm Hg]) than RCT patients. Registry patients presented more often via ambulance and had a similar total length of stay as RCT patients. In-hospital mortality was significantly higher in the registry compared with the RCT patients (9.3% versus 1.3%,
P
<0.001), and this remained after multivariable adjustment (odds ratio 6.6, 95% CI 2.6–16.8,
P
<0.001).

Conclusions—

Patients enrolled in a large RCT of acute heart failure differed significantly based on clinical characteristics, treatments, and inpatient outcomes from contemporaneous patients participating in a registry. These results highlight the need for context of RCTs to evaluate generalizability of results and especially the need to improve clinical outcomes in acute heart failure.

Clinical Trial Registration—

URL:
http://www.clinicaltrials.gov
. Unique identifier: NCT00475852.
Adenoid Ciliostimulation in Children with Chronic Otitis Media
Authors: Andreoli Steven M. , Schlosser Rodney J. , Wang Ling‐Feng , Mulligan Ryan M. , Discolo Christopher M. , White David R.
Published: October 2012

Objective

Adenoid hypertrophy and chronic adenoiditis are associated with an increased incidence of chronic otitis media. This study intends to determine the relationship between chronic otitis media and dynamic ciliary beat frequency in children undergoing adenoidectomy.

Study Design

Prospective, controlled study.

Setting

Pediatric tertiary care hospital.

Subjects and Methods

Children undergoing adenoidectomy were enrolled. Patients were stratified according to their indication for surgery, including adenotonsillar hypertrophy with obstructive sleep apnea, chronic otitis media with effusion, or recurrent episodes of acute otitis media. Adenoids were harvested using the curette. Tissue was sectioned and allowed to equilibrate in basal media for 24 hours. Cilia‐bearing tissue was then stimulated using isoproterenol or methacholine. Ciliary beat frequency was serially reordered and analyzed using the Sisson‐Ammons Video Analysis software program.

Results

Baseline ciliary beat frequency was similar in all groups (N = 47, total). Using isoproterenol, children with chronic otitis media with effusion demonstrated a blunted dynamic ciliary response at 2 and 3 hours relative to control (P =. 0176 and P =. 0282). Methacholine‐stimulated ciliary beat frequency was not different between each group.

Conclusion

At 2 and 3 hours following isoproterenol stimulation, there was a significant blunting of dynamic ciliary beat frequency in children with chronic otitis media with effusion. This ciliary dysfunction may provide a physiological explanation related to chronic adenoiditis in children with chronic otitis media.
Experiences and identities
Authors: Fletcher Tim
Published: October 2012

Shaping a professional identity is an important process in learning to teach. Case studies of Natasha and Julia, two pre-service elementary classroom teachers, were analysed to explore how they developed identities for teaching physical education during a pre-service teacher education programme. By critically analysing their physical education experiences and engaging in inclusive pedagogies, both challenged their prior assumptions of what teaching physical education entailed and meant to them. While both cases did not necessarily form identities that they believed were required to successfully teach physical education, they engaged in processes that allowed them to make small but important steps to shaping positive professional identities as teachers of physical education. Implications for preparing elementary classroom teachers to teach physical education are discussed in light of the findings.
Use of a chemically induced-colon carcinogenesis-prone Apc-mutant rat in a chemotherapeutic bioassay
Authors: Yoshimi Kazuto , Hashimoto Takao , Niwa Yusuke , Hata Kazuya , Serikawa Tadao , Tanaka Takuji , Kuramoto Takashi
Published: October 2012

Background

Chemotherapeutic bioassay for colorectal cancer (CRC) with a rat model bearing chemically-induced CRCs plays an important role in the development of new anti-tumor drugs and regimens. Although several protocols to induce CRCs have been developed, the incidence and number of CRCs are not much enough for the efficient bioassay. Recently, we established the very efficient system to induce CRCs with a chemically induced-colon carcinogenesis-prone Apc-mutant rat, Kyoto Apc Delta (KAD) rat. Here, we applied the KAD rat to the chemotherapeutic bioassay for CRC and showed the utility of the KAD rat.

Methods

The KAD rat has been developed by the ENU mutagenesis and carries a homozygous nonsense mutation in the Apc gene (S2523X). Male KAD rats were given a single subcutaneous injection of AOM (20 mg/kg body weight) at 5 weeks of age. Starting at 1 week after the AOM injection, they were given 2% DSS in drinking water for 7 days. Tumor-bearing KAD rats were divided into experimental and control groups on the basis of the number of tumors observed by endoscopy at week 8. The 5-fluorouracil (5-FU) was administrated intravenously a dose of 50 or 75 mg/kg weekly at week 9, 10, and 11. After one-week interval, the 5-FU was given again at week 13, 14, and 15. At week 16, animals were sacrificed and tumor number and volume were measured macroscopically and microscopically.

Results

In total 48 tumors were observed in 27 KAD rats with a 100% incidence at week 8. The maximum tolerated dose for the KAD rat was 50 mg/kg of 5-FU. Macroscopically, the number or volume of tumors in the 5-FU treated rats was not significantly different from the control. Microscopically, the number of adenocarcinoma in the 5-FU treated rats was not significantly different (p < 0.02) from that of the control. However, the volume of adenocarcinomas was significantly lower than in the control. Anticancer effect of the 5-FU could be obtained only after the 16 weeks of experimental period.

Conclusion

The use of the AOM/DSS-treated tumor-bearing KAD rats could shorten the experimental period and reduce the number of animals examined in the chemotherapeutic bioassay. The efficient bioassay with the AOM/DSS-treated tumor-bearing KAD rats would promote the development of new anti-tumor drugs and regimens.
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

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

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

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

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

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

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

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

ZnO 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

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

DNA 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

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

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

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.
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

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

Sequencing-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.