bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical properties of hybrid T3Pyr/SiO2/3C-SiC nanowires
Authors: Fabbri Filippo , Rossi Francesca , Melucci Manuela , Manet Ilse , Attolini Giovanni , Favaretto Laura , Zambianchi Massimo , Salviati Giancarlo 
Published: December 2012

Abstract
A new class of nanostructured hybrid materials is developed by direct grafting of a model thiophene-based organic dye on the surface of 3C-SiC/SiO2 core/shell nanowires. TEM-EDX analysis reveals that the carbon distribution is more spread than it would be, considering only the SiC core size, suggesting a main contribution from C of the oligothiophene framework. Further, the sulfur signal found along the treated wires is not detected in the as-grown samples. In addition, the fluorescent spectra are similar for the functionalized nanostructures and T3Pyr in solution, confirming homogeneous molecule grafting on the nanowire surface. Chemical and luminescence characterizations confirm a homogeneous functionalization of the nanowires. In particular, the fluorophore retains its optical properties after functionalization.
Cycling and bone health: a systematic review
Authors: Olmedillas Hugo , González-Agüero Alejandro , Moreno Luis A , Casajus José A , Vicente-Rodríguez Germán 
Published: December 2012

Abstract

Background
Cycling is considered to be a highly beneficial sport for significantly enhancing cardiovascular fitness in individuals, yet studies show little or no corresponding improvements in bone mass.

Methods
A scientific literature search on studies discussing bone mass and bone metabolism in cyclists was performed to collect all relevant published material up to April 2012. Descriptive, cross-sectional, longitudinal and interventional studies were all reviewed. Inclusion criteria were met by 31 studies.

Results
Heterogeneous studies in terms of gender, age, data source, group of comparison, cycling level or modality practiced among others factors showed minor but important differences in results. Despite some controversial results, it has been observed that adult road cyclists participating in regular training have low bone mineral density in key regions (for example, lumbar spine). Conversely, other types of cycling (such as mountain biking), or combination with other sports could reduce this unsafe effect. These results cannot yet be explained by differences in dietary patterns or endocrine factors.

Conclusions
From our comprehensive survey of the current available literature it can be concluded that road cycling does not appear to confer any significant osteogenic benefit. The cause of this may be related to spending long hours in a weight-supported position on the bike in combination with the necessary enforced recovery time that involves a large amount of time sitting or lying supine, especially at the competitive level.
Biologic activity of the novel small molecule STAT3 inhibitor LLL12 against canine osteosarcoma cell lines
Authors: Couto Jason I , Bear Misty D , Lin Jiayuh , Pennel Michael , Kulp Samuel K , Kisseberth William C , London Cheryl A 
Published: December 2012

AbstractBackgroundSTAT3 [1] has been shown to be dysregulated in nearly every major cancer, including osteosarcoma (OS). Constitutive activation of STAT3, via aberrant phosphorylation, leads to proliferation, cell survival and resistance to apoptosis. The present study sought to characterize the biologic activity of a novel allosteric STAT3 inhibitor, LLL12, in canine OS cell lines.ResultsWe evaluated the effects of LLL12 treatment on 4 canine OS cell lines and found that LLL12 inhibited proliferation, induced apoptosis, reduced STAT3 phosphorylation, and decreased the expression of several transcriptional targets of STAT3 in these cells. Lastly, LLL12 exhibited synergistic anti-proliferative activity with the chemotherapeutic doxorubicin in the OS lines.ConclusionLLL12 exhibits biologic activity against canine OS cell lines through inhibition of STAT3 related cellular functions supporting its potential use as a novel therapy for OS.
KL-6, a Human MUC1 Mucin, as a prognostic marker for diffuse alveolar hemorrhage syndrome
Authors: Kida Yoshiko , Ohshimo Shinichiro , Ota Kohei , Tamura Tomoko , Otani Tadatsugu , Une Kazunobu , Sadamori Takuma , Iwasaki Yasumasa , Bonella Francesco , Hattori Noboru , Hirohashi Nobuyuki , Guzman Josune , Costabel Ulrich , Kohno Nobuoki , Tanigawa Koichi 
Published: December 2012

AbstractBackgroundDiffuse alveolar hemorrhage syndrome is a life threatening condition with diverse etiologies. Sensitive prognostic markers for diffuse alveolar hemorrhage have not been well investigated. Serum KL-6 is a biomarker for various interstitial lung disease associated with disease activity and prognosis. The purpose of the present study was to evaluate the clinical utility of serum KL-6 level as a prognostic marker for diffuse alveolar hemorrhage.MethodsWe retrospectively collected 41 consecutive patients clinically diagnosed as having diffuse alveolar hemorrhage who were admitted to the Intensive Care Unit of Hiroshima University Hospital between 2004 and 2011. Correlation between prognosis and age, sex, laboratory findings including serum KL-6, radiological findings, ventilatory modes or therapeutic regimens were evaluated.ResultsBaseline and peak serum KL-6 levels were significantly higher in non-survivors compared with survivors. An increase in KL-6 levels during the initial week was associated with a subsequent deterioration of the oxygenation index. Higher baseline KL-6 levels and higher peak KL-6 levels were strongly correlated with death. With a cut-off level of 700 U/mL for peak KL-6, the sensitivity, specificity and accuracy for non-survival were 75%, 85% and 78%, respectively. In the multivariate analysis, only the peak KL-6 level ≥700 U/ml was an independent poor prognostic factor for diffuse alveolar hemorrhage.ConclusionsPeak serum KL-6 level ≥700 U/ml may become a clinically useful marker of poor prognosis for diffuse alveolar hemorrhage.
Mathematical modeling of left ventricular dimensional changes in mice during aging
Authors: Yang Tianyi , Chiao Ying Ann , Wang Yunji , Voorhees Andrew , Han Hai-Chao , Lindsey Merry L , Jin Yu-Fang 
Published: December 2012

Abstract
Cardiac aging is characterized by diastolic dysfunction of the left ventricle (LV), which is due in part to increased LV wall stiffness. In the diastolic phase, myocytes are relaxed and extracellular matrix (ECM) is a critical determinant to the changes of LV wall stiffness. To evaluate the effects of ECM composition on cardiac aging, we developed a mathematical model to predict LV dimension and wall stiffness changes in aging mice by integrating mechanical laws and our experimental results. We measured LV dimension, wall thickness, LV mass, and collagen content for wild type (WT) C57/BL6J mice of ages ranging from 7.3 months to those of 34.0 months. The model was established using the thick wall theory and stretch-induced tissue growth to an isotropic and homogeneous elastic composite with mixed constituents. The initial conditions of the simulation were set based on the data from the young mice. Matlab simulations of this mathematical model demonstrated that the model captured the major features of LV remodeling with age and closely approximated experimental results. Specifically, the temporal progression of the LV interior and exterior dimensions demonstrated the same trend and order-of-magnitude change as our experimental results. In conclusion, we present here a validated mathematical model of cardiac aging that applies the thick-wall theory and stretch-induced tissue growth to LV remodeling with age.
Genetic studies of complex human diseases: Characterizing SNP-disease associations using Bayesian networks
Authors: Han Bing , Chen Xue-wen , Talebizadeh Zohreh , Xu Hua 
Published: December 2012

Abstract

Background
Detecting epistatic interactions plays a significant role in improving pathogenesis, prevention, diagnosis, and treatment of complex human diseases. Applying machine learning or statistical methods to epistatic interaction detection will encounter some common problems, e.g., very limited number of samples, an extremely high search space, a large number of false positives, and ways to measure the association between disease markers and the phenotype.

Results
To address the problems of computational methods in epistatic interaction detection, we propose a score-based Bayesian network structure learning method, EpiBN, to detect epistatic interactions. We apply the proposed method to both simulated datasets and three real disease datasets. Experimental results on simulation data show that our method outperforms some other commonly-used methods in terms of power and sample-efficiency, and is especially suitable for detecting epistatic interactions with weak or no marginal effects. Furthermore, our method is scalable to real disease data.

Conclusions
We propose a Bayesian network-based method, EpiBN, to detect epistatic interactions. In EpiBN, we develop a new scoring function, which can reflect higher-order epistatic interactions by estimating the model complexity from data, and apply a fast Branch-and-Bound algorithm to learn the structure of a two-layer Bayesian network containing only one target node. To make our method scalable to real data, we propose the use of a Markov chain Monte Carlo (MCMC) method to perform the screening process. Applications of the proposed method to some real GWAS (genome-wide association studies) datasets may provide helpful insights into understanding the genetic basis of Age-related Macular Degeneration, late-onset Alzheimer's disease, and autism.
Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome
Authors: Wang Yajun , Yu Yao , Pan Bohu , Hao Pei , Li Yixue , Shao Zhifeng , Xu Xiaogang , Li Xuan 
Published: December 2012

Abstract

Background
Sequencing of bacterial genomes became an essential approach to study pathogen virulence and the phylogenetic relationship among close related strains. Bacterium Enterococcus faecium emerged as an important nosocomial pathogen that were often associated with resistance to common antibiotics in hospitals. With highly divergent gene contents, it presented a challenge to the next generation sequencing (NGS) technologies featuring high-throughput and shorter read-length. This study was designed to investigate the properties and systematic biases of NGS technologies and evaluate critical parameters influencing the outcomes of hybrid assemblies using combinations of NGS data.

Results
A hospital strain of E. faecium was sequenced using three different NGS platforms: 454 GS-FLX, Illumina GAIIx, and ABI SOLiD4.0, to approximately 28-, 500-, and 400-fold coverage depth. We built a pipeline that merged contigs from each NGS data into hybrid assemblies. The results revealed that each single NGS assembly had a ceiling in continuity that could not be overcome by simply increasing data coverage depth. Each NGS technology displayed some intrinsic properties, i.e. base calling error, systematic bias, etc. The gaps and low coverage regions of each NGS assembly were associated with lower GC contents. In order to optimize the hybrid assembly approach, we tested with varying amount and different combination of NGS data, and obtained optimal conditions for assembly continuity. We also, for the first time, showed that SOLiD data could help make much improved assemblies of E. faecium genome using the hybrid approach when combined with other type of NGS data.

Conclusions
The current study addressed the difficult issue of how to most effectively construct a complete microbial genome using today's state of the art sequencing technologies. We characterized the sequence data and genome assembly from each NGS technologies, tested conditions for hybrid assembly with combinations of NGS data, and obtained optimized parameters for achieving most cost-efficiency assembly. Our study helped form some guidelines to direct genomic work on other microorganisms, thus have important practical implications.
Induction of cytokines in different organs after intranasal inoculation of Campylobacter jejuni in mice
Authors: Al-Banna Nadia A , Raghupathy Raj , Albert M John 
Published: December 2012

Abstract

Background
Cytokine production and histopathological changes occur in the lungs of mice after intranasal inoculation with Campylobacter jejuni, but the levels of cytokines in different organs to which C. jejuni disseminates have not been studied.

Findings
Adult BALB/c mice were intranasally inoculated with C. jejuni 81– 176 (test) or phosphate-buffered saline (control) (n=16 per group). The levels of cytokines in the organs (spleen, liver, and small and large intestines) to which C. jejuni disseminated were measured by ELISA. Two cytokine patterns were observed. First, increased proinflammatory cytokines, TNF-α, IL-1, and IL-2, were followed by anti-inflammatory cytokines, IL-4 and IL-10 in the spleen and large intestine. Second, in the liver and small intestine, there was a predominant production of anti-inflammatory cytokines, IL-4 and IL-10, with some increase in IL-2 levels. In the spleen and intestines, the levels of pro- and anti-inflammatory cytokines were concurrently increased.

Conclusion
Dissemination of C. jejuni is associated with the production of different cytokine profiles in different tissues, with the proinflammatory response appearing in the spleen and large intestine at an earlier time point than in the liver and small intestine. The organs produce different cytokine profiles in response to C. jejuni dissemination. These preliminary findings should be confirmed with a study involving a larger group of animals.
Persistent inter‐industry wage differences: rent sharing and opportunity costs
Authors: Abowd John M , Kramarz Francis , Lengermann Paul , McKinney Kevin L , Roux Sébastien 
Published: December 2012

Abstract

Abstract
We reconsider the potential for explaining inter‐industry wage differences by decomposing those differences into parts due to individual and employer heterogeneity, respectively. Using longitudinally linked employer‐employee data, we estimate the model for the United States and France. The part arising from individual heterogeneity can be theoretically and empirically related to the worker’s opportunity wage rate. The part arising from employer heterogeneity can similarly be related to product market quasi‐rents and relative bargaining power. We find that these two variables are highly correlated with both parts of the differential in France. Although the U.S. inter‐industry wage differentials are strongly correlated with those in France, the decomposition is more nuanced in the American data, where the opportunity wage rate and the product market conditions are related to both the personal and employer heterogeneity.

JEL codes
J31, J50, L10
Optimizing positive end-expiratory pressure by oscillatory mechanics minimizes tidal recruitment and distension: an experimental study in a lavage model of lung injury
Authors: Zannin Emanuela , Dellaca Raffaele L , Kostic Peter , Pompilio Pasquale P , Larsson Anders , Pedotti Antonio , Hedenstierna Goran , Frykholm Peter 
Published: December 2012

Abstract
Introduction
It is well established that during mechanical ventilation of patients with acute respiratory distress syndrome cyclic recruitment/derecruitment and overdistension are potentially injurious for lung tissues. We evaluated whether the forced oscillation technique (FOT) could be used to guide the ventilator settings in order to minimize cyclic lung recruitment/derecruitment and cyclic mechanical stress in an experimental model of acute lung injury.

Methods
We studied six pigs in which lung injury was induced by bronchoalveolar lavage. The animals were ventilated with a tidal volume of 6 ml/kg. Forced oscillations at 5 Hz were superimposed on the ventilation waveform. Pressure and flow were measured at the tip and at the inlet of the endotracheal tube respectively. Respiratory system reactance (Xrs) was computed from the pressure and flow signals and expressed in terms of oscillatory elastance (EX5). Positive end-expiratory pressure (PEEP) was increased from 0 to 24 cm H2O in steps of 4 cm H2O and subsequently decreased from 24 to 0 in steps of 2 cm H2O. At each PEEP step CT scans and EX5 were assessed at end-expiration and end-inspiration.

Results
During deflation the relationship between both end-expiratory and end-inspiratory EX5 and PEEP was a U-shaped curve with minimum values at PEEP = 13.4 ± 1.0 cm H2O (mean ± SD) and 13.0 ± 1.0 cm H2O respectively. EX5 was always higher at end-inspiration than at end-expiration, the difference between the average curves being minimal at 12 cm H2O. At this PEEP level, CT did not show any substantial sign of intra-tidal recruitment/derecruitment or expiratory lung collapse.

Conclusions
Using FOT it was possible to measure EX5 both at end-expiration and at end-inspiration. The optimal PEEP strategy based on end-expiratory EX5 minimized intra-tidal recruitment/derecruitment as assessed by CT, and the concurrent attenuation of intra-tidal variations of EX5 suggests that it may also minimize tidal mechanical stress.
Risk factors for dementia after critical illness in elderly medicare beneficiaries
Authors: Guerra Carmen , Linde-Zwirble Walter T , Wunsch Hannah 
Published: December 2012

Abstract
Introduction
Hospitalization increases the risk of a subsequent diagnosis of dementia. We aimed to identify diagnoses or events during a hospitalization requiring critical care that are associated with a subsequent dementia diagnosis in the elderly.

Methods
A cohort study of a random 5% sample of Medicare beneficiaries who received intensive care in 2005 and survived to hospital discharge, with three years of follow-up (through 2008) was conducted using Medicare claims files. We defined dementia using the International Classification of Diseases, 9th edition, clinical modification (ICD-9-CM) codes and excluded patients with any prior diagnosis of dementia or cognitive impairment in the year prior to admission. We used an extended Cox model to examine the association between diagnoses and events associated with the critical illness and a subsequent diagnosis of dementia, adjusting for known risk factors for dementia.

Results
Over the three years of follow-up, dementia was newly diagnosed in 4,519 (17.8%) of 25,368 patients who received intensive care and survived to hospital discharge. After accounting for known risk factors, having an infection (adjusted hazard ratio (AHR) = 1.25; 95% CI, 1.17 to 1.35), or a diagnosis of severe sepsis (AHR = 1.40; 95% CI, 1.28 to 1.53), acute neurologic dysfunction (AHR = 2.06; 95% CI, 1.72 to 2.46), and acute dialysis (AHR = 1.70; 95% CI, 1.30 to 2.23) were all independently associated with a subsequent diagnosis of dementia. No other measured ICU factors, such as need for mechanical ventilation, were independently associated.

Conclusions
Among ICU events, infection or severe sepsis, neurologic dysfunction, and acute dialysis were independently associated with a subsequent diagnosis of dementia. Patient prognostication, as well as future research into post-ICU cognitive decline, should focus on these higher-risk subgroups.
Brain-derived neurotrophic factor plasma levels are associated with mortality in critically ill patients even in the absence of brain injury
Authors: Ritter Cristiane , Miranda Aline S , Giombelli Vinícius Renê , Tomasi Cristiane D , Comim Clarissa M , Teixeira Antonio Lucio , Quevedo João , Dal-Pizzol Felipe 
Published: December 2012

Abstract
Introduction
Because of its relevance to the functioning of the central nervous system, brain-derived neurotrophic factor (BDNF) has been implicated in the pathogenesis of different neuropsychiatric diseases. Whether the BDNF level can be a marker of brain dysfunction and thus predict mortality in critically ill patients is not known. Thus we aimed to determine whether the plasma levels of BDNF are associated with morbidity and mortality in critically ill patients.

Methods
Healthy volunteers (n = 40) and consecutive patients older than 18 years (n = 76) admitted for more than 24 hours in an Intensive Care Unit (ICU) in a University hospital between July and October 2010 were included in the present study. First blood samples were collected within 12 hours of enrollment (D0), and a second sample, 48 hours after (D2) for determination of plasma BDNF levels. The relation between BDNF levels and mortality was the primary outcome. The secondary outcomes were the relation between BDNF levels and delirium and coma-free days (DCFD) and ICU and hospital length of stay (LOS).

Results
Admission plasma levels of BDNF were higher in ICU patients when compared with healthy volunteers (1,536 (962) versus 6,565 (2,838) pg/ml). The mean BDNF D2 was significantly lower in nonsurvivor patients (5,865 (2,662) versus 6,741 (2,356) pg/ml). After adjusting for covariates, BDNF levels, the need for mechanical ventilation, and sepsis were associated with mortality. Even in patients without clinically detectable brain dysfunction, lower BDNF D2 levels were associated with mortality. BDNF D2 had a mild correlation to DCFD (r = 0.44), but not to ICU and hospital LOS. In addition, plasma BDNF did not correlate to different plasma cytokines and platelets levels.

Conclusions
The plasma levels of BDNF were independently associated with mortality, even in the absence of clinically detectable brain dysfunction.
Natural variation of H3K27me3 distribution between two Arabidopsis accessions and its association with flanking transposable elements
Authors: Dong Xue , Reimer Julia , Göbel Ulrike , Engelhorn Julia , He Fei , Schoof Heiko , Turck Franziska 
Published: December 2012

Abstract
Background
Histone H3 lysine 27 tri-methylation and lysine 9 di-methylation are independent repressive chromatin modifications in Arabidopsis thaliana. H3K27me3 is established and maintained by Polycomb repressive complexes whereas H3K9me2 is catalyzed by SUVH histone methyltransferases. Both modifications can spread to flanking regions after initialization and were shown to be mutually exclusive in Arabidopsis.

Results
We analyzed the extent of natural variation of H3K27me3 in the two accessions Landsberg erecta (Ler) and Columbia (Col) and their F1 hybrids. The majority of H3K27me3 target genes in Col were unchanged in Ler and F1 hybrids. A small number of Ler-specific targets were detected and confirmed. Consistent with a cis-regulatory mechanism for establishing H3K27me3, differential targets showed allele-specific H3K27me3 in hybrids. Five Ler-specific targets showed the active mark H3K4me3 in Col and for this group, differential H3K27me3 enrichment accorded to expression variation. On the other hand, the majority of Ler-specific targets were not expressed in Col, Ler or 17 other accessions. Instead of H3K27me3, the antagonistic mark H3K9me2 and other heterochromatic features were observed at these loci in Col. These loci were frequently flanked by transposable elements, which were often missing in the Ler genome assembly.

Conclusion
There is little variation in H3K27me3 occupancy within the species, although H3K27me3 targets were previously shown as overrepresented among differentially expressed genes. The existing variation in H3K27me3 seems mostly explained by flanking polymorphic transposable elements. These could nucleate heterochromatin, which then spreads into neighboring H3K27me3 genes, thus converting them to H3K9me2 targets.