bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying elemental genomic track types and representing them uniformly
Authors: Gundersen Sveinung , Kalaš Matúš , Abul Osman , Frigessi Arnoldo , Hovig Eivind , Sandve Geir Kjetil
Published: December 2011

Background

With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, are rapidly being generated in an increasing number of laboratories. The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that are easy to parse. A host of alternative formats are currently available and in use, complicating analysis and tool development. The issue of whether and how the multitude of formats reflects varying underlying characteristics of data has to our knowledge not previously been systematically treated.

Results

We here identify intrinsic distinctions between genomic features, and argue that the distinctions imply that a certain variation in the representation of features as genomic tracks is warranted. Four core informational properties of tracks are discussed: gaps, lengths, values and interconnections. From this we delineate fifteen generic track types. Based on the track type distinctions, we characterize major existing representational formats and find that the track types are not adequately supported by any single format. We also find, in contrast to the XML formats, that none of the existing tabular formats are conveniently extendable to support all track types. We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0.

Conclusions

The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience.
Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers
Authors: Parker Hugo J , Piccinelli Paul , Sauka-Spengler Tatjana , Bronner Marianne , Elgar Greg
Published: December 2011

Background

Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them.

Results

Here, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs) through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development.

Conclusions

These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs), which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution.
Selectively enhanced expression of prophenoloxidase activating enzyme 1 (PPAE1) at a bacteria clearance site in the white shrimp, Litopenaeus vannamei
Authors: Jang In-Kwon , Pang Zhenguo , Yu Jiaping , Kim Su-Kyoung , Seo Hyung-Cheol , Cho Yeong-Rok
Published: December 2011

Background

The prophenoloxidase-activating (PO activating) system plays an important role in the crustacean innate immunity, particularly in wound healing and pathogen defense. A key member of this system is prophenoloxidase-activating enzyme (PPAE), which is the direct activator of prophenoloxidase (proPO). Despite their importance in crustacean PO activating system, the studies on them remain limited.

Results

Here we report on a PPAE of white shrimp, Litopenaeus vannamei (lvPPAE1), which showed 94% similarity to PPAE1 of Penaeus monodon. We found that lvPPAE1 in fluid hemocytes was down regulated after challenge by Vibrio harveyi but was enhanced when shrimps were exposed to a bacteria-rich environment for long-term. In vivo gene silence of lvPPAE1 by RNAi can significantly reduce the phenoloxidase activity (PO) and increase the susceptibility of shrimps to V. harveyi. Although lvPPAE1 was down-regulated in fluid hemocytes by Vibrio challenge, its expression increased significantly in gill after bacteria injection, which is the primary bacteria-clearance tissue.

Conclusion

Suppressed expression in fluid hemocytes and enhanced expression in gill indicates selectively enhanced expression at the bacterial clearance site. This is a novel feature for PPAE expression. The results will contribute to our understanding of the PO activating system in crustaceans.
C-reactive protein is an independent predictor for carotid artery intima-media thickness progression in asymptomatic younger adults (from the Bogalusa Heart Study)
Authors: Toprak Ahmet , Kandavar Ramprasad , Toprak Demet , Chen Wei , Srinivasan Sathanur , Xu Ji Hua , Anwar Asif , Berenson Gerald S
Published: December 2011

Background

Conflicting information exists regarding the association between hsCRP and the progression of early stages of atherosclerosis. The purpose of the study was to investigate the association of high sensitiviy c-reactive protein (hsCRP) along with major cardiovascular (CV) risk factors on early carotid atherosclerosis progression in a large, population-based cohort study.

Methods

The study cohort included 839 young adults (aged 24 to 43 years, 70% white, 42% men) enrolled in Bogalusa Heart Study, who in 2001-2002 attended baseline examination with measurements of CV risk factors. Progression of carotid artery intima-media thickness (IMT) was assessed during a mean follow-up of 2.4 years.

Results

Carotid artery IMT progression rates were as follows: composite carotid artery = 9.2 ± 52 μm/y, common carotid artery = 0.0 ± 51 μm/y, carotid bulb = 8.8 ± 103 μm/y, and internal carotid artery = 18.9 ± 81 μm/y. Elevated baseline hsCRP, reflecting an inflammatory state, showed independent association with composite carotid artery IMT progression. Increased age, systolic blood pressure, fasting glucose, LDL cholesterol, and current smoking were other risk associates of carotid artery IMT progression in young adults, indicating an underlying burden on the CV system by multiple risk factors.

Conclusion

In this population-based study, we observed independent categorical association of increased hsCRP with carotid artery IMT progression in young adults. This study underlines the importance of assesssing hsCRP levels along with smoking and traditional CV risk factor profiles in asymptomatic young adults.
Etomidate and mortality in cirrhotic patients with septic shock
Authors: Cherfan Antoine J , Tamim Hani M , AlJumah Abdulrahman , Rishu Asgar H , Al-Abdulkareem Abdulmajeed , Al Knawy Bandar A , Hajeer Ali , Tamimi Waleed , Brits Riette , Arabi Yaseen M
Published: December 2011

Background

Clinical effects and outcomes of a single dose etomidate prior to intubation in the intensive care setting is controversial. The aim of this study is to evaluate the association of a single dose effect of etomidate prior to intubation on the mortality of septic cirrhotic patients and the impact of the subsequent use of low dose hydrocortisone.

Methods

This is a nested-cohort study within a randomized double blind placebo controlled study evaluating the use of low dose hydrocortisone in cirrhotic septic patients. Cirrhotic septic patients ≥ 18 years were included in the study. Patients who received etomidate prior to intubation were compared to those who did not receive etomidate for all cause 28-day mortality as a primary outcome.

Results

Sixty two intubated patients out of the 75 patients randomized in the initial trial were eligible for this study. Twenty three of the 62 intubated patients received etomidate dose prior to intubation. Etomidate use was not associated with all cause 28-day mortality or hospital mortality but was associated with significantly higher ICU mortality (91% vs. 64% for etomidate and controls groups, respectively; p = 0.02). Etomidate patients who received subsequent doses of hydrocortisone required lower doses of vasopressors and had more vasopressor-free days but no improvement in mortality.

Conclusions

In this group of septic cirrhotic patients with very high mortality, etomidate increased ICU mortality. Subsequent use of hydrocortisone appears to have no benefit beyond decreasing vasopressor requirements. The lowest mortality was observed in patients who did not receive etomidate but received hydrocortisone.
Perception of health risks of electromagnetic fields by MRI radiographers and airport security officers compared to the general Dutch working population: a cross sectional analysis
Authors: van Dongen Diana , Smid Tjabe , Timmermans Daniëlle RM
Published: December 2011

Background

The amount of exposure to electromagnetic fields (EMF) at work is mainly determined by an individual's occupation and may differ from exposure at home. It is, however, unknown how different occupational groups perceive possible adverse health effects of EMF.

Methods

Three occupational groups, the general Dutch working population (n = 567), airport security officers who work with metal detectors (n = 106), and MRI radiographers who work with MRI (n = 193), were compared on perceived risk of and positive and negative feelings towards EMF in general and of different EMF sources, and health concerns by using analyses of variances. Data were collected via an internet survey.

Results

Overall, MRI radiographers had a lower perceived risk, felt less negative, and more positive towards EMF and different sources of EMF than the general working population and the security officers. For security officers, feeling more positive about EMF was not significantly related to perceived risk of EMF in general or EMF of domestic sources. Feeling positive about a source did not generalize to a lower perceived risk, while negative feelings were stronger related to perceived risk. MRI radiographers had fewer health concerns regarding EMF than the other two groups, although they considered it more likely that EMF could cause physical complaints.

Conclusions

These data show that although differences in occupation appear to be reflected in different perceptions of EMF, the level of occupational exposure to EMF as such does not predict the perceived health risk of EMF.
S100A10 protein expression is associated with oxaliplatin sensitivity in human colorectal cancer cells
Authors: Suzuki Sayo , Yamayoshi Yasuko , Nishimuta Akito , Tanigawara Yusuke
Published: December 2011

Background

Individual responses to oxaliplatin (L-OHP)-based chemotherapy remain unpredictable. The objective of our study was to find candidate protein markers for tumor sensitivity to L-OHP from intracellular proteins of human colorectal cancer (CRC) cell lines. We performed expression difference mapping (EDM) analysis of whole cell lysates from 11 human CRC cell lines with different sensitivities to L-OHP by using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), and identified a candidate protein by liquid chromatography/mass spectrometry ion trap time-of-flight (LCMS-IT-TOF).

Results

Of the qualified mass peaks obtained by EDM analysis, 41 proteins were differentially expressed in 11 human colorectal cancer cell lines. Among these proteins, the peak intensity of 11.1 kDa protein was strongly correlated with the L-OHP sensitivity (50% inhibitory concentrations) (P < 0.001, R

2
= 0.80). We identified this protein as Protein S100-A10 (S100A10) by MS/MS ion search using LCMS-IT-TOF. We verified its differential expression and the correlation between S100A10 protein expression levels in drug-untreated CRC cells and their L-OHP sensitivities by Western blot analyses. In addition, S100A10 protein expression levels were not correlated with sensitivity to 5-fluorouracil, suggesting that S100A10 is more specific to L-OHP than to 5-fluorouracil in CRC cells. S100A10 was detected in cell culture supernatant, suggesting secretion out of cells.

Conclusions

By proteomic approaches including SELDI technology, we have demonstrated that intracellular S100A10 protein expression levels in drug-untreated CRC cells differ according to cell lines and are significantly correlated with sensitivity of CRC cells to L-OHP exposure. Our findings provide a new clue to searching predictive markers of the response to L-OHP, suggesting that S100A10 is expected to be one of the candidate protein markers.
Poly I: C-activated dendritic cells that were generated in CellGro for use in cancer immunotherapy trials
Authors: Fučíková Jitka , Rožková Daniela , Ulčová Hana , Budinský Vít , Sochorová Klára , Pokorná Kateřina , Bartůňková Jiřina , Špíšek Radek
Published: December 2011

Background

For clinical applications, dendritic cells (DCs) need to be generated using GMP-approved reagents. In this study, we tested the characteristics of DCs generated in two clinical grade culture media and activated by three maturation stimuli, Poly I: C, LPS and the mixture of proinflammatory cytokines in order to identify the optimal combination of culture media and activation stimulus for the clinical use.

Method

We tested DCs generation using two GMP-certified culture media, CellGro and RPMI+5% human AB serum and evaluated DCs morphology, viability and capapability to mature. We tested three maturation stimuli, PolyI:C, LPS and the mixture of proinflammatory cytokines consisting of IL-1, IL-6, TNF and prostaglandin E2. We evaluated the capacity of activated DCs to induce antigen-specific T cells and regulatory T lymphocytes.

Results

Cell culture in CellGro resulted in a higher yield of immature DCs resulting from increased number of adherent monocytes. DCs that were generated in CellGro and activated using Poly I:C were the most efficient in expanding antigen-specific T cells compared to the DCs that were generated in other media and activated using LPS or the cocktail of proinflammatory cytokines. A comparison of all tested combinations revealed that DCs that were generated in CellGro and activated using Poly I:C induced low numbers of regulatory T cells.

Conclusion

In this study, we identified monocyte-derived DCs that were generated in CellGro and activated using Poly I:C as the most potent clinical-grade DCs for the induction of antigen-specific T cells.
Weak convergence theorem for the three-step iterations of non-Lipschitzian nonself mappings in Banach spaces
Authors: Zhu Lanping , Huang Qianglian , Chen Xiaoru
Published: December 2011

In this article, we introduce a new three-step iterative scheme for the mappings which are asymptotically nonexpansive in the intermediate sense in Banach spaces. Weak convergence theorem is established for this three-step iterative scheme in a uniformly convex Banach space that satisfies Opial's condition or whose dual space has the Kadec-Klee property. Furthermore, we give an example of the nonself mapping which is asymptotically nonexpansive in the intermediate sense but not asymptotically nonexpansive. The results obtained in this article extend and improve many recent results in this area.

AMS classification: 47H10; 47H09; 46B20.
Shape matters: effects of silver nanospheres and wires on human alveolar epithelial cells
Authors: Stoehr Linda C , Gonzalez Edgar , Stampfl Andreas , Casals Eudald , Duschl Albert , Puntes Victor , Oostingh Gertie J
Published: December 2011

Background

In nanotoxicology, the exact role of particle shape, in relation to the composition, on the capacity to induce toxicity is largely unknown. We investigated the toxic and immunotoxic effects of silver wires (length: 1.5 - 25 μm; diameter 100 - 160 nm), spherical silver nanoparticles (30 nm) and silver microparticles (<45 μm) on alveolar epithelial cells (A549).

Methods

Wires and nanoparticles were synthesized by wet-chemistry methods and extensively characterized. Cell viability and cytotoxicity were assessed and potential immunotoxic effects were investigated. To compare the effects on an activated and a resting immune system, cells were stimulated with rhTNF-α or left untreated. Changes in intracellular free calcium levels were determined using calcium imaging. Finally, ion release from the particles was assessed by ICP-MS and the effects of released ions on cell viability and cytotoxicity were tested.

Results

No effects were observed for the spherical particles, whereas the silver wires significantly reduced cell viability and increased LDH release from A549 cells. Cytokine promoter induction and NF-κB activation decreased in a concentration dependent manner similar to the decrease seen in cell viability. In addition, a strong increase of intracellular calcium levels within minutes after addition of wires was observed. This toxicity was not due to free silver ions, since the samples with the highest ion release did not induce toxicity and ion release control experiments with cells treated with pre-incubated medium did not show any effects either.

Conclusions

These data showed that silver wires strongly affect the alveolar epithelial cells, whereas spherical silver particles had no effect. This supports the hypothesis that shape is one of the important factors that determine particle toxicity.
Difficulty accessing crack pipes and crack pipe sharing among people who use drugs in Vancouver, Canada
Authors: Ti Lianping , Buxton Jane , Wood Evan , Zhang Ruth , Montaner Julio , Kerr Thomas
Published: December 2011

Background

Crack pipe sharing can increase health risks among people who use drugs, yet the reasons for sharing these pipes have not been well described. Therefore, we sought to identify the prevalence and correlates of crack pipe sharing among a community-recruited sample of people who use illicit drugs in Vancouver, a setting where crack pipes are provided at low or no cost.

Findings

Data for this study were derived from two prospective cohorts of people who use drugs: the Vancouver Injection Drug Users Study (VIDUS) and the AIDS Care Cohort to evaluate Exposure to Survival Services (ACCESS). Multivariate logistic regression was used to identify factors independently associated with crack pipe sharing. Among 503 crack users, 238 (47.3%) participants reported having shared a crack pipe in the previous six months. Having acquired a mouthpiece in the last six months (adjusted odds ratio [AOR] = 1.91; 95% confidence interval [CI]: 1.31 - 2.79) and difficulty finding new pipes (AOR = 2.19; 95%CI: 1.42 - 3.37) were positively associated with pipe sharing. Binge drug use (AOR = 1.39; 95%CI: 0.96 - 2.02) was marginally associated with sharing pipes.

Discussion

There was a high prevalence of crack pipe sharing in a setting where crack pipes are distributed at low or no cost. Difficulty accessing crack pipes was independently and positively associated with this behavior. These findings suggest that additional efforts are needed to discourage crack pipe sharing as well as increase access to crack pipes.
Early peroxisome proliferator-activated receptor gamma regulated genes involved in expansion of pancreatic beta cell mass
Authors: Vivas Yurena , Martínez-García Cristina , Izquierdo Adriana , Garcia-Garcia Francisco , Callejas Sergio , Velasco Ismael , Campbell Mark , Ros Manuel , Dopazo Ana , Dopazo Joaquin , Vidal-Puig Antonio , Medina-Gomez Gema
Published: December 2011

Background

The progression towards type 2 diabetes depends on the allostatic response of pancreatic beta cells to synthesise and secrete enough insulin to compensate for insulin resistance. The endocrine pancreas is a plastic tissue able to expand or regress in response to the requirements imposed by physiological and pathophysiological states associated to insulin resistance such as pregnancy, obesity or ageing, but the mechanisms mediating beta cell mass expansion in these scenarios are not well defined. We have recently shown that ob/ob mice with genetic ablation of PPARγ2, a mouse model known as the POKO mouse failed to expand its beta cell mass. This phenotype contrasted with the appropriate expansion of the beta cell mass observed in their obese littermate ob/ob mice. Thus, comparison of these models islets particularly at early ages could provide some new insights on early PPARγ dependent transcriptional responses involved in the process of beta cell mass expansion

Results

Here we have investigated PPARγ dependent transcriptional responses occurring during the early stages of beta cell adaptation to insulin resistance in wild type, ob/ob, PPARγ2 KO and POKO mice. We have identified genes known to regulate both the rate of proliferation and the survival signals of beta cells. Moreover we have also identified new pathways induced in ob/ob islets that remained unchanged in POKO islets, suggesting an important role for PPARγ in maintenance/activation of mechanisms essential for the continued function of the beta cell.

Conclusions

Our data suggest that the expansion of beta cell mass observed in ob/ob islets is associated with the activation of an immune response that fails to occur in POKO islets. We have also indentified other PPARγ dependent differentially regulated pathways including cholesterol biosynthesis, apoptosis through TGF-β signaling and decreased oxidative phosphorylation.
Occurrence of the invasion associated marker (iam) in Campylobacter jejuni isolated from cattle
Authors: Sanad Yasser M , Kassem Issmat I , Liu Zhe , Lin Jun , LeJeune Jeffrey T , Rajashekara Gireesh
Published: December 2011

Background

The invasion associated marker (iam) has been detected in the majority of invasive Campylobacter jejuni retrieved from humans. Furthermore, the detection of iam in C. jejuni isolated from two important hosts, humans and chickens, suggested a role for this marker in C. jejuni's colonization of multiple hosts. However, no data exist regarding the occurrence of this marker in C. jejuni isolated from non-poultry food-animals such as cattle, an increasingly important source for human infections. Since little is known about the genetics associated with C. jejuni's capability for colonizing physiologically disparate hosts, we investigated the occurrence of the iam in C. jejuni isolated from cattle and assessed the potential of iam-containing cattle and human isolates for chicken colonization and human cell invasion.

Results

Simultaneous RAPD typing and iam-specific PCR analysis of 129 C. jejuni isolated from 1171 cattle fecal samples showed that 8 (6.2%) of the isolates were iam-positive, while 7 (54%) of human-associated isolates were iam-positive. The iam sequences were mostly heterogeneous and occurred in diverse genetic backgrounds. All iam-positive isolates were motile and possessed important genes (cad F, cia B, cdt B) associated with adhesion and virulence. Although certain iam-containing isolates invaded and survived in INT-407 cells in high numbers and successfully colonized live chickens, there was no clear association between the occurrence, allelic sequence, and expression levels of the iam and the aforementioned phenotypes.

Conclusions

We show that the prevalence of iam in cattle C. jejuni is relatively lower as compared to isolates occurring in humans and chickens. In addition, iam was polymorphic and certain alleles occur in cattle isolates that were capable of colonizing and invading chickens and human intestinal cells, respectively. However, the iam did not appear to contribute to the cattle-associated C. jejuni's potential for invasion and intracellular survival in human intestinal cells as well as chicken colonization.
Effect of an integrated control strategy for schistosomiasis japonica in the lower reaches of the Yangtze River, China: an evaluation from 2005 to 2008
Authors: Sun Le-Ping , Wang Wei , Liang You-Sheng , Tian Zeng-Xi , Hong Qing-Biao , Yang Kun , Yang Guo-Jing , Dai Jian-Rong , Gao Yang
Published: December 2011

Background

Schistosomiasis japonica remains a major public health concern in China. There are many interventions implemented to control the transmission of the disease. The purpose of the present study was to investigate the effects of an integrated control strategy for schistosomiasis control.

Methods

An integrated control strategy for schistosomiasis japonica with emphasis on removing cattle from snail-infested grasslands, providing farmers with mechanized farm equipment, improving sanitation by supplying tap water and building lavatories and latrines and providing boats with fecal-matter containers was implemented in 107 villages of the lower reaches of the Yangtze River, Jiangsu Province, China, during a 32-month period from May 2005 to 2008, and the effectiveness was investigated.

Results

Following the effects of the comprehensive control, the snail habitat, infected snail habitat, snail infection rate, and S. japonicum prevalence in both humans and livestock all appeared a declining trend year by year, with reductions of 47.88%, 94.29%, 92.55%, 96.94%, and 100% compared with those before the comprehensive control. In addition, all of the 17 counties achieved the infection control in 2007, and 7 reached the criteria of transmission control in 2008. The confirmed snail habitats reduced from 107 to 20, and the acute infections have also been controlled for 2 successive years since 2007.

Conclusions

The integrated control strategy for schistosomiasis japonica is effective to control the transmission of S. japonicum.
Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera
Authors: Mendum Tom A , Newcombe Jane , Mannan Ahmad A , Kierzek Andrzej M , McFadden Johnjoe
Published: December 2011

Background

Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequences are available for several strains but our understanding of how these data relate to phenotype remains limited.

Results

To investigate the metabolism of N. meningitidis we generated and then selected a representative Tn5 library on rich medium, a minimal defined medium and in human serum to identify genes essential for growth under these conditions. To relate these data to a systems-wide understanding of the pathogen's biology we constructed a genome-scale metabolic network: Nmb_iTM560. This model was able to distinguish essential and non-essential genes as predicted by the global mutagenesis. These essentiality data, the library and the Nmb_iTM560 model are powerful and widely applicable resources for the study of meningococcal metabolism and physiology. We demonstrate the utility of these resources by predicting and demonstrating metabolic requirements on minimal medium, such as a requirement for phosphoenolpyruvate carboxylase, and by describing the nutritional and biochemical status of N. meningitidis when grown in serum, including a requirement for both the synthesis and transport of amino acids.

Conclusions

This study describes the application of a genome scale transposon library combined with an experimentally validated genome-scale metabolic network of N. meningitidis to identify essential genes and provide novel insight into the pathogen's metabolism both in vitro and during infection.
Synthesis, Characterization, and OFET and OLED Properties of π-Extended Ladder-Type Heteroacenes Based on Indolodibenzothiophene
Authors: Wang Changsheng , Nishida Jun-ichi , Bryce Martin R , Yamashita Yoshiro
Published: December 2011

Ladder-type heteroacenes based on indolodibenzothiophene have been synthesized. The route involved a regioselective twofold intramolecular acid-induced cyclization of the central bis(butylsulfinyl)phenyl unit onto the adjacent carbazole units, followed by dealkylation to give diindolobenzobisbenzothiophene (DIBBBT) derivatives. Importantly, this sequence proceeded efficiently in the presence of the chloro substituents which provided reactive sites for further π-extension of the DIBBBT core. The chloro derivative underwent twofold palladium-catalyzed Suzuki–Miyaura reactions with phenylboronic acid or 4-n-octylphenylboronic acid. Compounds have been characterized by 1H NMR spectroscopy, mass spectrometry, elemental analysis, optical spectroscopy, and solution electrochemical studies. Organic field-effect transistors (OFETs) have been constructed based on drop-cast thin films and the performances as p-type semiconductor are presented. The chloro derivative was also copolymerized with 9,9-dioctyl-2,7-fluorenylenediboronic acid bis(1,3-propanediol) ester to give the alternating copolymer which exhibits blue photoluminescence in solution and blue-green electroluminescence in a solution processed organic light-emitting diode (OLED).
Diversity analysis of pseudomonads in rice rhizosphere for multifaceted plant growth promotion
Authors: Naganandini Srinivasan , Balachandar Dananjeyan , Kumar Krishnamoorthy
Published: December 2011

This investigation was carried out based on the hypothesis that there may be some pseudomonad strains, which could exist in rhizosphere of plant species contributing multifaceted beneficial activities. For this purpose, 21 pseudomonad isolates from the rhizosphere of rice, cultivated in western parts of Tamil Nadu were screened. All the 21 isolates were authenticated as pseudomonads by a genus-specific PCR screening. The molecular diversity of these isolates was investigated by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and the dendrogram obtained from the analysis revealed that all the 21 isolates clustered into seven groups. Further, these isolates were screened for plant growth promoting activities such as diazotrophy (PCR amplification of nifH gene and acetylene reduction assay), Indole acetic acid (IAA) and siderophore production (spectrometrically), 1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase for ethylene regulation (PCR screening), mineral solubilization (biochemically) and antagonistic potential against soil pathogenic fungi (dual culture assay). Based on the results, two elite Pseudomonas isolates (S9 and O3) were chosen as multi-functional plant growth-promoting rhizobacteria, paving way for potential use as bioinoculants in rice.
Aetiology of upper respiratory tract infections in children in Arak City: A community based study
Authors: Kahbazi Manijeh , Fahmizad Alireza , Armin Shahnaz , Ghanaee Roxana , Fallah Fateme , Shiva Faride , Golnabi Akram , Jahromy Mana , Arjomandzadegan Mohammad , Karimi Abdollah
Published: December 2011

Viruses are frequent causes of upper respiratory tract infections in children. We investigated the viral aetiology of community-acquired upper respiratory tract infections (URIs) in young children treated as outpatients in community settings.During November 2008, nasal swab specimens were taken from children with recent onset of upper respiratory tract infections. The patients attended day care or primary schools; the specimens were randomly obtained by pediatricians from schools and childcare institutions and sent for identification by PCR method.A total of 300 specimens were collected. From all samples, 40.67% were positive for at least 1 virus, viz. adenovirus 11.76%, rhinovirus 9.8%, respiratory syncytial virus 6.08%, influenza virus 5.56%, parainfluenza virus 4.9%, enterovirus 2.94% and a combination of 2 viruses 2%. Clinical manifestations of the respiratory infections were as follows: 70.7% of the patients had coryza, 69.3% cough, 26% sneezing, 19.7% sore throat, 2.7% headache, 7.7% fever, 2.3% conjunctivitis, 1.3% abdominal pain and 1% hoarseness.The results of this study demonstrate that adenoviruses and rhinoviruses are the two most common viral agents isolated from pediatric outpatients with acute URIs in autumn in Arak City. Coryza and cough were the most common symptoms in children. Sore throat and hoarseness were more prevalent in infections caused by influenza virus, conjunctivitis in parainfluenza, and coryza in rhinovirus infections.
Liver abscess as the presenting manifestation of chronic granulomatous disease
Authors: Mamishi Setareh , Ahmadi Faezeh , Ahmadi Maedeh , Rezaei Nima
Published: December 2011

Chronic granulomatous disease (CGD) is a rare primary immunodeficiency disease, affecting phagocytic blood cells, which predispose patients to recurrent infectious complications. Herein, an 11-year-old girl is described who presented with liver abscess at the age of 9 years. Positive dihydrorhodamine (DHR) and nitrobluetetrazolium (NBT) tests confirmed the diagnosis of CGD for the patient. Anti-tuberculosis drugs and parenteral antibiotic therapy were started. Unusual visceral abscess and recurrent infections should be considered as an alarm for primary immunodeficiency diseases, while early diagnosis and appropriate treatment could prevent severe complications and even death in this group of patients.
Human cytomegalovirus induces MMP-1 and MMP-3 expression in aortic smooth muscle cells
Authors: Prochnau Dirk , Lehmann Marc , Straube Eberhard , Figulla Hans , Rödel Jürgen
Published: December 2011

Human cytomegalovirus (HCMV) infection may be involved in the pathogenesis of atherosclerosis by modulating functions of smooth muscle cells (SMC). In this study, we performed an oligonucleotide microarray screening of 780 inflammation-associated genes in HCMV-infected aortic SMC (AoSMC). The expression of 31 genes was stimulated and 24 genes were down-regulated following infection with HCMV strain DC-134. Following infection with HCMV strain AD-169 infection, we found 24 genes to be stimulated and 32 genes to be down-regulated. Among these were primarily genes encoding for CC and CXC chemokines, adhesion molecules, and tumor necrosis factor (TNF) receptor superfamily members, apoptosis-related factors, signal transduction molecules and transcription regulators. The up-regulated genes included matrix metalloproteinase (MMP)-1 and MMP-3 in HCMV infected cells. Using RT-PCR and enzyme immunoassay we found stimulated expression of MMP-1 (3.2-fold expression) and MMP-3 (334-fold expression) in HCMV strain DC-134-infected AoSMC at 72 h following infection.The findings of our study suggest that HCMV infection of AoSMC cause an activation of atherosclerosis-relevant factors in SMC. The increased expression of MMPs which have been shown to be involved in atherosclerotic plaque rupture and myocardial infarction is in agreement with the hypothesis that this pathogen might contribute to plaque inflammation in atherosclerotic disease.
Impression Techniques for Multiple Implants: A Photoelastic Analysis. Part II: Comparison of Four Acrylic Resins
Authors: Lopes-Júnior Itamar , de Lima Lucas Barbara , Gomide Henner Alberto , Gomes Vanderlei Luiz
Published: December 2011

Four commercial brands of chemically activated acrylic resin were compared through photoelastic analysis. Photoelastic resin blocks were made with 2 implants placed parallel to each other and 2 square transfer copings splinted. Both transfers were splinted with chemically activated acrylic resin: Dencrilay, Duralay I, Duralay II, and GC. Data were analyzed by 2-way analysis of variance and Tukey test (P < .05). Statistically significant differences were found among the 3 brands of chemically activated acrylic resin. Dencrilay showed greater dimensional alteration. Duralay I and GC are recommended for the transfer of the position of the multi-implants.
Peri-Implant Biomechanical Responses to Standard, Short-Wide, and Mini Implants Supporting Single Crowns Under Axial and Off-Axial Loading (an In Vitro Study)
Authors: Kheiralla Lamia Sayed , Younis Jihan Farouk
Published: December 2011

This study compared the biomechanical responses of 3 single crowns supported by 3 different implants under axial and off-axial loading. A standard implant (3.75 mm diameter, 13 mm length), a mini implant (3 mm diameter, 13 mm length), and a short-wide implant (5.7 mm diameter, 8 mm length) were embedded in epoxy resin by the aid of a surveyor to ensure their parallelism. Each implant supported a full metal crown made of Ni-Cr alloy with standardized dimensions. Strain gauges and finite element analysis (FEA) were used to measure the strain induced under axial and off-axial functional loads of 300 N. Results showed that mini implants recorded the highest microstrains, under both axial and off-axial loading. All implants showed a considerable increase in strain values under off-axial loading. Standard and short-wide implants proved to be preferable in supporting crowns, as the standard implant showed the lowest strains under axial and off-axial loading using FEA simulation, while the short-wide implant showed the lowest strains under nonaxial loading using strain gauge analysis.
Photoelastic Analysis of Stress Distribution With Different Implant Systems
Authors: Pellizzer Eduardo Piza , Carli Rafael Imai , Falcón-Antenucci Rosse Mary , Verri Fellippo Ramos , Goiato Marcelo Coelho , Villa Luiz Marcelo Ribeiro
Published: December 2011

The aim of this study was to evaluate stress distribution with different implant systems through photoelasticity. Five models were fabricated with photoelastic resin PL-2. Each model was composed of a block of photoelastic resin (10 × 40 × 45 mm) with an implant and a healing abutment: model 1, internal hexagon implant (4.0 × 10 mm; Conect AR, Conexão, São Paulo, Brazil); model 2, Morse taper/internal octagon implant (4.1 × 10 mm; Standard, Straumann ITI, Andover, Mass); model 3, Morse taper implant (4.0 × 10 mm; AR Morse, Conexão); model 4, locking taper implant (4.0 × 11 mm; Bicon, Boston, Mass); model 5, external hexagon implant (4.0 × 10 mm; Master Screw, Conexão). Axial and oblique load (45°) of 150 N were applied by a universal testing machine (EMIC-DL 3000), and a circular polariscope was used to visualize the stress. The results were photographed and analyzed qualitatively using Adobe Photoshop software. For the axial load, the greatest stress concentration was exhibited in the cervical and apical thirds. However, the highest number of isochromatic fringes was observed in the implant apex and in the cervical adjacent to the load direction in all models for the oblique load. Model 2 (Morse taper, internal octagon, Straumann ITI) presented the lowest stress concentration, while model 5 (external hexagon, Master Screw, Conexão) exhibited the greatest stress. It was concluded that Morse taper implants presented a more favorable stress distribution among the test groups. The external hexagon implant showed the highest stress concentration. Oblique load generated the highest stress in all models analyzed.
Single Stage Immediate Implant Placements in the Esthetic Zone
Authors: Yong Loong T.
Published: December 2011

This case series report documents 5 successful cases of immediate implant placements into fresh extraction sockets in the esthetic zone, subsequently restored with favourable outcomes. The case selection, treatment planning, surgical protocol, restorative outcomes are presented and discussed.
Benefits and Safety of Long-Term Fenofibrate Therapy in People With Type 2 Diabetes and Renal Impairment
Authors: Ting Ru-Dee , Keech Anthony C. , Drury Paul L. , Donoghoe Mark W. , Hedley John , Jenkins Alicia J. , Davis Timothy M.E. , Lehto Seppo , Celermajer David , Simes R. John , Rajamani Kushwin , Stanton Kim ,   on behalf of the FIELD Study Investigators
Published: December 2011

OBJECTIVE

Diabetic patients with moderate renal impairment (estimated glomerular filtration rate [eGFR] 30–59 mL/min/1.73 m2) are at particular cardiovascular risk. Fenofibrate’s safety in these patients is an issue because it may elevate plasma creatinine. Furthermore, guidelines regarding fenofibrate dosing in renal impairment vary internationally. We investigated fenofibrate’s effects on cardiovascular and end-stage renal disease (ESRD) events, according to eGFR, in the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) Study.

RESEARCH DESIGN AND METHODS

Type 2 diabetic patients (aged 50–75 years) with eGFR ≥30 mL/min/1.73 m2 were randomly allocated to a fixed dose of fenofibrate (200 mg daily) (n = 4,895) or placebo (n = 4,900) for 5 years. Baseline renal function (Modification of Diet in Renal Disease equation) was grouped by eGFR (30–59, 60–89, and ≥90 mL/min/1.73 m2). The prespecified outcome was total cardiovascular events (composite of cardiovascular death, myocardial infarction, stroke, and coronary/carotid revascularization). Serious adverse events and instances of ESRD (plasma creatinine >400 μmol/L, dialysis, renal transplant, or renal death) were recorded. Analysis was by intention to treat.

RESULTS

Overall, fenofibrate reduced total cardiovascular events, compared with placebo (hazard ratio 0.89 [95% CI 0.80–0.99]; P = 0.035). This benefit was not statistically different across eGFR groupings (P = 0.2 for interaction) (eGFR 30–59 mL/min/1.73 m2: 0.68 [0.47–0.97], P = 0.035; eGFR ≥90 mL/min/1.73 m2: 0.85 [0.70–1.02], P = 0.08). ESRD rates were similar between treatment arms, without adverse safety signals of fenofibrate use in renal impairment.

CONCLUSIONS

Patients with type 2 diabetes and moderate renal impairment benefit from long-term fenofibrate, without excess drug-related safety concerns compared with those with no or mild renal impairment. Fenofibrate treatment should not be contraindicated in moderate renal impairment, suggesting that current guidelines may be too restrictive.
A new BSMV-based vector with modified β molecule allows simultaneous and stable silencing of two genes
Authors: Kawalek Adam , Dmochowska-Boguta Marta , Nadolska-Orczyk Anna , Orczyk Waclaw
Published: December 2011

Virus-induced gene silencing is an important tool for functional gene analysis and the vector based on Barley stripe mosaic virus (BSMV) is widely used for the purpose in monocots. Of the tripartite BSMV genome, currently the BSMV:γMCS molecule is used to clone a fragment of a target gene. As an alternative, the BSMV:β molecule was engineered with a unique BamHI site between the open reading frame of βc (ORF βc) and poly(A). The mixture of RNA particles α, βBamHI and γMCS was fully infectious. Barley phytoene desaturase and wheat phospholipase Dα fragments were cloned to βBamHI and γMCS. Delivery of the target gene fragment in γMCS induced stronger silencing, while delivery in βBamHI yielded more stable transcript reduction. A quantitative analysis (qRT-PCR) of the transcripts showed that the silencing induced with a fragment carried in both particles was stronger and more stable than that from a fragment placed in one particle. The modification of β enables simultaneous silencing of two genes. Quantifying the β and γ particles in virus-inoculated plants revealed a 2.5-fold higher level of γ than β, while the stability of the insert was higher in β compared with γ. The possible influence of the relative quantity of β and γ particles in virus-inoculated plants on insert stability and gene silencing efficiency is discussed.
Inhibition of biogenic membrane flippase activity in reconstituted ER proteoliposomes in the presence of low cholesterol levels
Authors: Rajasekharan Archita , Gummadi Sathyanarayana
Published: December 2011

Biogenic membranes or self-synthesizing membranes are the site of synthesis of new lipids such as the endoplasmic reticulum (ER) in eukaryotes. Newly synthesized phospholipids (PLs) at the cytosolic leaflet of ER need to be translocated to the lumen side for membrane biogenesis and this is facilitated by a special class of lipid translocators called biogenic membrane flippase. Even though ER is the major site of cholesterol synthesis, it contains very low amounts of cholesterol, since newly synthesized cholesterol in ER is rapidly transported to other organelles and is highly enriched in plasma membrane. Thus, only low levels of cholesterol are present at the biosynthetic compartment (ER), which results in loose packing of ER lipids. We hypothesize that the prevalence of cholesterol in biogenic membranes might affect the rapid flip-flop. To validate our hypothesis, detergent solubilized ER membranes from both bovine liver and spinach leaves were reconstituted into proteoliposomes with varying mol% of cholesterol. Our results show that (i) with increase in the cholesterol/PL ratio, the half-life time of PL translocation increased, suggesting that cholesterol affects the kinetics of flipping, (ii) flipping activity was completely inhibited in proteoliposomes reconstituted with 1 mol% cholesterol, and (iii) FRAP and DSC experiments revealed that 1 mol% cholesterol did not alter the bilayer properties significantly and that flippase activity inhibition is probably mediated by interaction of cholesterol with the protein.
Cloning and expression of a new inositol 1,4,5-trisphosphate receptor type 1 splice variant in adult rat atrial myocytes
Authors: Subedi Krishna , Singh Thoudam , Kim Joon-Chul , Woo Sun-Hee
Published: December 2011

Inositol 1,4,5-trisphosphate receptor type 1 (IP3R1) is already known to be highly expressed in the brain, and is found in many other tissues, including the atrium of the heart. Although the complete primary structure of IP3R1 in the rat brain has been reported, the complete sequence of an IP3R1 clone from atrial myocytes has not been reported. We isolated an IP3R1 complementary DNA (cDNA) clone from isolated adult rat atrial myocytes, and found a new splice variant of IP3R1 that was different from a previously reported IP3R1 cDNA clone obtained from a rat brain (NCBI GenBank accession number: NM_001007235). Our clone had 99% similarity with the rat brain IP3R1 sequence; the exceptions were 39 amino acid deletions at the position of 1693–1731, and the deletion of phenylalanine at position 1372 that lay in the regulatory region. Compared with the rat brain IP3R1, in our clone proline was replaced with serine at residue 2439, and alanine was substituted for valine at residue 2445. These changes lie adjacent to or within the fifth transmembrane domain (2440–2462). Although such changes in the amino acid sequences were different from the rat brain IP3R1 clone, they were conserved in human or mouse IP3R1. We produced a plasmid construct expressing the atrial IP3R1 together with green fluorescent protein (GFP), and successfully overexpressed the atrial IP3R1 in the adult atrial cell line HL-1. Further investigation is needed on the physiological significance of the new splice variant in atrial cell function.
Uniqueness of meromorphic functions concerning fixed points
Authors: Wang Li-Qin , Luo Xu-Dan
Published: December 2011

In this paper, we discuss the uniqueness of meromorphic functions concerning fixed points. In view of the fixed points, we extend a recent conclusion due to Zhang and Lin. Moreover, under the condition of f and g sharing ∞ IM, our theorem generalizes some previous results of Fang and Qiu, Lin and Yi and so on.
On T points of algebroid functions
Authors: Wu Nan , Xuan Zu-xing
Published: December 2011

In this paper, we firstly give a new definition, namely, the T point of algebroid functions. Then by using Ahlfors’ theory of covering surfaces, we prove the existence of these points for any ν-valued algebroid functions in the unit disk satisfying $\mathop {\lim \sup }\limits_{r \to 1^ - } \frac{{T(r,w)}}
{{\log \tfrac{1}
{{1 - r}}}} = + \infty
$. This extends the recent results of Xuan, Wu and Sun.