bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reducing LPS content in cockroach allergens increases pulmonary cytokine production without increasing inflammation: A randomized laboratory study
Authors: Natarajan Sudha , Kim Jiyoun , Bouchard Jacqueline , Cruikshank William , Remick Daniel G 
Published: February 2011

AbstractBackgroundEndotoxins are ubiquitously present in the environment and constitute a significant component of ambient air. These substances have been shown to modulate the allergic response, however a consensus has yet to be reached whether they attenuate or exacerbate asthmatic responses. The current investigation examined whether reducing the concentration of lipopolysaccharide (LPS) in a house dust extract (HDE) containing high concentrations of both cockroach allergens [1] and LPS would attenuate asthma-like pulmonary inflammation.MethodsMice were sensitized with CRA and challenged with the intact HDE, containing 182 ng of LPS, or an LPS-reduced HDE containing 3 ng LPS, but an equivalent amount of CRA. Multiple parameters of asthma-like pulmonary inflammation were measured.ResultsCompared to HDE challenged mice, the LPS-reduced HDE challenged mice had significantly reduced TNFα levels in the bronchoalveolar lavage fluid. Plasma levels of IgE and IgG1 were significantly reduced, however no change in CRA-specific IgE was detected. In HDE mice, plasma IgG2a levels were similar to naïve mice, while LPS-reduced HDE mice had significantly greater concentrations. Reduced levels of LPS in the HDE did not decrease eosinophil or neutrophil recruitment into the alveolar space. Equivalent inflammatory cell recruitment occurred despite having generally higher pulmonary concentrations of eotaxins and CXC chemokines in the LPS-reduced HDE group. LPS-reduced HDE challenge induced significantly higher concentrations of IFNγ, and IL-5 and IL-13 in the BAL fluid, but did not decrease airways hyperresponsiveness or airway resistance to methacholine challenge.Conclusion:These data show that reduction of LPS levels in the HDE does not significantly protect against the severity of asthma-like pulmonary inflammation.
Identifying and characterizing COPD patients in US managed care. A retrospective, cross-sectional analysis of administrative claims data
Authors: Mapel Douglas W , Dutro Michael P , Marton Jenő P , Woodruff Kimberly , Make Barry 
Published: February 2011

Abstract

Background
Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death among US adults and is projected to be the third by 2020. In anticipation of the increasing burden imposed on healthcare systems and payers by patients with COPD, a means of identifying COPD patients who incur higher healthcare utilization and costs is needed.

Methods
This retrospective, cross-sectional analysis of US managed care administrative claims data describes a practical way to identify COPD patients. We analyze 7.79 million members for potential inclusion in the COPD cohort, who were continuously eligible during a 1-year study period. A younger commercial population (7.7 million) is compared with an older Medicare population (0.115 million). We outline a novel approach to stratifying COPD patients using "complexity" of illness, based on occurrence of claims for given comorbid conditions. Additionally, a unique algorithm was developed to identify and stratify COPD exacerbations using claims data.

Results
A total of 42,565 commercial (median age 56 years; 51.4% female) and 8507 Medicare patients (median 75 years; 53.1% female) were identified as having COPD. Important differences were observed in comorbidities between the younger commercial versus the older Medicare population. Stratifying by complexity, 45.0%, 33.6%, and 21.4% of commercial patients and 36.6%, 35.8%, and 27.6% of older patients were low, moderate, and high, respectively. A higher proportion of patients with high complexity disease experienced multiple (≥2) exacerbations (61.7% commercial; 49.0% Medicare) than patients with moderate- (56.9%; 41.6%), or low-complexity disease (33.4%; 20.5%). Utilization of healthcare services also increased with an increase in complexity.

Conclusion
In patients with COPD identified from Medicare or commercial claims data, there is a relationship between complexity as determined by pulmonary and non-pulmonary comorbid conditions and the prevalence of exacerbations and utilization of healthcare services. Identification of COPD patients at highest risk of exacerbations using complexity stratification may facilitate improved disease management by targeting those most in need of treatment.
Reduced risk for placental malaria in iron deficient women
Authors: Senga Edward L , Harper Gregory , Koshy Gibby , Kazembe Peter N , Brabin Bernard J 
Published: February 2011

Abstract

Background
Nutritional iron deficiency may limit iron availability to the malaria parasite reducing infection risk, and/or impair host immunity thereby increasing this risk. In pregnant women, there is evidence of an adverse effect with iron supplementation, but the few reported studies are strongly confounded.

Methods
A case control study in pregnant Malawian women was undertaken in Chikhwawa southern Malawi in order to describe iron status in relation to placental malaria controlling for several confounding factors. Pregnancy characteristics were obtained and a blood sample at delivery. A full blood count was performed and serum ferritin and transferrin receptor quantified by enzyme-linked immunoassay. DNA analysis was used to identify genetic polymorphisms for ABO phenotype, hemoglobin HbS, and glucose -6 phosphate dehydrogenase deficiency. Placental tissue was obtained and malaria histology classified as active, past or no malaria infection.

Results
112 cases with placental malaria were identified and 110 women with no evidence of placental infection. Iron deficiency was less frequent in women with placental Plasmodium falciparum infection. In those with acute, chronic or past placental infections the odds ratio for iron deficiency was 0.4, 95% CI 0.2-0.8, p = 0.01; for acute and chronic infections 0.4, 0.2-0.8, p = 0.006; for acute infection 0.3, 0.1-0.7, p = 0.001. The association was greater in multigravidae.

Conclusion
Women with either acute, or acute and chronic placental malaria were less likely to have iron deficiency than women without placental malaria infection There is a priority to establish if reversing iron deficiency through iron supplementation programs either prior to or during pregnancy enhances malaria risk.
Low density lipoprotein receptor gene Ava II polymorphism and serum lipid levels in the Guangxi Bai Ku Yao and Han populations
Authors: Long Xing-Jiang , Yin Rui-Xing , Li Ke-La , Liu Wan-Ying , Zhang Lin , Cao Xiao-Li , Miao Lin , Wu Dong-Feng , Htet Aung Lynn Htet , Hu Xi-Jiang 
Published: February 2011

Abstract

Background
Several common genetic polymorphisms in the low density lipoprotein receptor (LDL-R) gene have associated with modifications of serum total cholesterol (TC) and low density lipoprotein cholesterol (LDL-C) levels, but the results are not consistent in different populations. Bai Ku Yao is a special subgroup of the Yao minority in China. The present study was undertaken to detect the association of LDL-R gene Ava ║ polymorphism and serum lipid levels in the Guangxi Bai Ku Yao and Han populations.

Methods
A total of 1024 subjects of Bai Ku Yao and 792 participants of Han Chinese were randomly selected from our previous stratified randomized cluster samples. Genotyping of the LDL-R gene Ava ║ polymorphism was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing.

Results
The levels of serum TC, high density lipoprotein cholesterol (HDL-C), LDL-C, apolipoprotein (Apo) A1 and the ratio of ApoA1 to ApoB were lower in Bai Ku Yao than in Han (P < 0.01 for all). The frequency of A- and A+ alleles was 65.5% and 34.5% in Bai Ku Yao, and 80.7% and 19.3% in Han (P < 0.001); respectively. The frequency of A-A-, A-A+ and A+A+ genotypes was 42.6%, 45.9% and 11.5% in Bai Ku Yao, and 64.9%, 31.6% and 3.5% in Han (P < 0.001); respectively. There was also significant difference in the genotypic frequencies between males and females in Bai Ku Yao (P <0.05), and in the genotypic and allelic frequencies between normal LDL-C (≤ 3.20 mmol/L) and high LDL-C (>3.20 mmol/L) subgroups in Bai Ku Yao (P < 0.05 for each) and between males and females in Han (P < 0.05 for each). The levels of LDL-C in males and TC and HDL-C in females were different among the three genotypes (P < 0.05 for all) in Bai Ku Yao, whereas the levels of HDL-C in males and HDL-C and ApoA1 in females were different among the three genotypes (P < 0.05-0.001) in Han. The subjects with A+A+ genotype had higher serum LDL-C, TC, HDL-C or ApoA1 levels than the subjects with A-A+ and A-A- genotypes. Spearman rank correlation analysis revealed that the levels of LDL-C in Bai Ku Yao and HDL-C in Han were correlated with genotypes (P < 0.05 and P < 0.01; respectively).

Conclusions
The association of LDL-R gene Ava ║ polymorphism and serum lipid levels is different between the Bai Ku Yao and Han populations. The discrepancy might partly result from different LDL-R gene Ava ║ polymorphism or LDL-R gene-enviromental interactions.
On the nature of the stretched exponential photoluminescence decay for silicon nanocrystals
Authors: Zatryb G , Podhorodecki A , Misiewicz J , Cardin J , Gourbilleau F 
Published: February 2011

AbstractThe influence of hydrogen rate on optical properties of silicon nanocrystals deposited by sputtering method was studied by means of time-resolved photoluminescence spectroscopy as well as transmission and reflection measurements. It was found that photoluminescence decay is strongly non-single exponential and can be described by the stretched exponential function. It was also shown that effective decay rate probability density function may be recovered by means of Stehfest algorithm. Moreover, it was proposed that the observed broadening of obtained decay rate distributions reflects the disorder in the samples.
Memory effects in annealed hybrid gold nanoparticles/block copolymer bilayers
Authors: Torrisi Vanna , Ruffino Francesco , Licciardello Antonino , Grimaldi Maria Grazia , Marletta Giovanni 
Published: February 2011

AbstractWe report on the use of the self-organization process of sputtered gold nanoparticles on a self-assembled block copolymer film deposited by horizontal precipitation Langmuir-Blodgett (HP-LB) method. The morphology and the phase-separation of a film of poly-n-butylacrylate-block-polyacrylic acid (Pn BuA-b-PAA) were studied at the nanometric scale by using atomic force microscopy (AFM) and Time of Flight Secondary Ion Mass Spectrometry (TOF-SIMS). The templating capability of the Pn BuA-b-PAA phase-separated film was studied by sputtering gold nanoparticles (NPs), forming a film of nanometric thickness. The effect of the polymer chain mobility onto the organization of gold nanoparticle layer was assessed by heating the obtained hybrid Pn BuA-b-PAA/Au NPs bilayer at T >Tg. The nanoparticles' distribution onto the different copolymer domains was found strongly affected by the annealing treatment, showing a peculiar memory effect, which modifies the AFM phase response of the Au NPs layer onto the polar domains, without affecting their surfacial composition. The effect is discussed in terms of the peculiar morphological features induced by enhanced mobility of polymer chains on the Au NPs layer.
Electrical behavior of MIS devices based on Si nanoclusters embedded in SiO
x
N
y
and SiO2 films
Authors: Jacques Emmanuel , Pichon Laurent , Debieu Olivier , Gourbilleau Fabrice 
Published: February 2011

AbstractWe examined and compared the electrical properties of silica (SiO2) and silicon oxynitride (SiO
x
N
y
) layers embedding silicon nanoclusters (Sinc) integrated in metal-insulator-semiconductor (MIS) devices. The technique used for the deposition of such layers is the reactive magnetron sputtering of a pure SiO2 target under a mixture of hydrogen/argon plasma in which nitrogen is incorporated in the case of SiO
x
N
y
layer. Al/SiO
x
N
y
-Sinc/p-Si and Al/SiO2-Sinc/p-Si devices were fabricated and electrically characterized. Results showed a high rectification ratio (>104) for the SiO
x
N
y
-based device and a resistive behavior when nitrogen was not incorporating (SiO2-based device). For rectifier devices, the ideality factor depends on the SiO
x
N
y
layer thickness. The conduction mechanisms of both MIS diode structures were studied by analyzing thermal and bias dependences of the carriers transport in relation with the nitrogen content.
Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes
Authors: Wang Dapeng , Liu Fei , Wang Lei , Huang Shi , Yu Jun 
Published: February 2011

Abstract

Background
Mammalian genome sequence data are being acquired in large quantities and at enormous speeds. We now have a tremendous opportunity to better understand which genes are the most variable or conserved, and what their particular functions and evolutionary dynamics are, through comparative genomics.

Results
We chose human and eleven other high-coverage mammalian genome data–as well as an avian genome as an outgroup–to analyze orthologous protein-coding genes using nonsynonymous (Ka) and synonymous (Ks) substitution rates. After evaluating eight commonly-used methods of Ka and Ks calculation, we observed that these methods yielded a nearly uniform result when estimating Ka, but not Ks (or Ka/Ks). When sorting genes based on Ka, we noticed that fast-evolving and slow-evolving genes often belonged to different functional classes, with respect to species-specificity and lineage-specificity. In particular, we identified two functional classes of genes in the acquired immune system. Fast-evolving genes coded for signal-transducing proteins, such as receptors, ligands, cytokines, and CDs (cluster of differentiation, mostly surface proteins), whereas the slow-evolving genes were for function-modulating proteins, such as kinases and adaptor proteins. In addition, among slow-evolving genes that had functions related to the central nervous system, neurodegenerative disease-related pathways were enriched significantly in most mammalian species. We also confirmed that gene expression was negatively correlated with evolution rate, i.e. slow-evolving genes were expressed at higher levels than fast-evolving genes. Our results indicated that the functional specializations of the three major mammalian clades were: sensory perception and oncogenesis in primates, reproduction and hormone regulation in large mammals, and immunity and angiotensin in rodents.

Conclusion
Our study suggests that Ka calculation, which is less biased compared to Ks and Ka/Ks, can be used as a parameter to sort genes by evolution rate and can also provide a way to categorize common protein functions and define their interaction networks, either pair-wise or in defined lineages or subgroups. Evaluating gene evolution based on Ka and Ks calculations can be done with large datasets, such as mammalian genomes.

Reviewers
This article has been reviewed by Drs. Anamaria Necsulea (nominated by Nicolas Galtier), Subhajyoti De (nominated by Sarah Teichmann) and Claus O. Wilke.
Accurate inference of shoot biomass from high-throughput images of cereal plants
Authors: Golzarian Mahmood R , Frick Ross A , Rajendran Karthika , Berger Bettina , Roy Stuart , Tester Mark , Lun Desmond S 
Published: February 2011

Abstract
With the establishment of advanced technology facilities for high throughput plant phenotyping, the problem of estimating plant biomass of individual plants from their two dimensional images is becoming increasingly important. The approach predominantly cited in literature is to estimate the biomass of a plant as a linear function of the projected shoot area of plants in the images. However, the estimation error from this model, which is solely a function of projected shoot area, is large, prohibiting accurate estimation of the biomass of plants, particularly for the salt-stressed plants. In this paper, we propose a method based on plant specific weight for improving the accuracy of the linear model and reducing the estimation bias (the difference between actual shoot dry weight and the value of the shoot dry weight estimated with a predictive model). For the proposed method in this study, we modeled the plant shoot dry weight as a function of plant area and plant age. The data used for developing our model and comparing the results with the linear model were collected from a completely randomized block design experiment. A total of 320 plants from two bread wheat varieties were grown in a supported hydroponics system in a greenhouse. The plants were exposed to two levels of hydroponic salt treatments (NaCl at 0 and 100 mM) for 6 weeks. Five harvests were carried out. Each time 64 randomly selected plants were imaged and then harvested to measure the shoot fresh weight and shoot dry weight. The results of statistical analysis showed that with our proposed method, most of the observed variance can be explained, and moreover only a small difference between actual and estimated shoot dry weight was obtained. The low estimation bias indicates that our proposed method can be used to estimate biomass of individual plants regardless of what variety the plant is and what salt treatment has been applied. We validated this model on an independent set of barley data. The technique presented in this paper may extend to other plants and types of stresses.
Surgical management of pulmonary inflammatory pseudotumors: A single center experience
Authors: Mondello Baldassare , Lentini Salvatore , Barone Mario , Barresi Pietro , Monaco Francesco , Familiari Dario , La Rocca Annunziata , Sibilio Michele , Acri Ignazio Eduardo , David Antonio , Monaco Maurizio 
Published: February 2011

Abstract

Background
The pulmonary inflammatory pseudotumor (PIP) is a rare disease. It is still debated whether it represents an inflammatory lesion characterized by uncontrolled cell growth or a true neoplasm. PIP is characterized by a cellular polymorphism.

Methods
We retrospectively analyzed 8 patients with PIP treated by surgery between 2001 and 2009. Preoperative thoracic computed tomography (CT) scan was performed in all cases. All patients underwent preoperative bronchoscopy with washing and brushing and/or transbronchial biopsy and preoperative cytology examination

Results
There were 5 men and 3 women, aged between 38 and 69 years (mean of 58 years). 3 patients (37%) were asymptomatic. The others had symptoms characterized by chest pain, shortness of breath and persistent cough or hemoptysis. 5 patients had neutrophilic leucocytosis. CT scan demonstrated solitary nodules (maximum diameter <3 cm) in 5 patients (62%) and lung masses (maximum diameter >3 cm) in 3 patients (37%). In 2 patients there were signs of pleural infiltration. Distant lesions were excluded in all cases. A preoperative histology examination failed to reach a definitive diagnosis in all patients. At surgery, we performed two lobectomies, one segmentectomy and five wedge resections, these being performed with videothoracoscopy (VATS), except for one patient where open surgery was used. Complete tumor resection was obtained in all patients. According to the Matsubara classification, there were 2 cases of organizing pneumonia, 5 cases of fibrous histiocytoma and one case of lymphoplasmacytoma. All patients were discharged alive from hospital between 4 and 7 days after surgery. At follow-up CT scan performed annually (range 11 to 112 months) (mean 58 months), there were no residual lesions, neither local nor distant recurrences.

Conclusions
PIP is a rare disease. Many synonyms have been used for this disease, usually in relation to the most represented cell type. The true incidence is unclear. Preoperative diagnosis is difficult to reach, despite performing a bronchoscopy or a transparietal needle aspiration. Different classifications have been proposed for PIP. Either medical, radiation or surgical therapy has been used for PIP. Whenever possible, surgery should be considered the standard treatment. Complete surgical resection is advocated to prevent recurrence.
Chemical fingerprinting and quantitative analysis of a Panax notoginseng preparation using HPLC-UV and HPLC-MS
Authors: Yao Hong , Shi Peiying , Shao Qing , Fan Xiaohui 
Published: February 2011

Abstract

Background
Xuesaitong (XST) injection, consisting of total saponins from Panax notoginseng, was widely used for the treatment of cardio- and cerebro-vascular diseases in China. This study develops a simple and global quality evaluation method for the quality control of XST.

Methods
High performance liquid chromatography-ultraviolet detection (HPLC-UV) was used to identify and quantify the chromatographic fingerprints of the XST injection. Characteristic common peaks were identified using HPLC with photo diode array detection/electrospray ionization tandem mass spectrometry (HPLC-PDA/ESI-MSn).

Results
Representative fingerprints from ten batches of samples showed 27 'common saponins' all of which were identified and quantified using ten reference saponins.

Conclusion
Chemical fingerprinting and quantitative analysis identified most of the common saponins for the quality control of P. notoginseng products such as the XST injection.
Extracellular domain of CD98hc is required for early murine development
Authors: Sato Yukiyasu , Heimeier Rachel A , Li Cuiling , Deng Chuxia , Shi Yun-Bo 
Published: February 2011

AbstractBackgroundThe multifunctional protein CD98 heavy chain (CD98hc, Slc3a2) associates with integrin β1 through its cytoplasmic and transmembrane domains and the CD98hc-mediated integrin signaling is required for maintenance of ES cell proliferation. CD98hc-null mice exhibit early post-implantation lethality similar to integrin β1-null mice, supporting the importance of its interaction with integrin β1. On the other hand, the extracellular domain of CD98hc interacts with L-type amino acid transporters (LATs) and is essential for appropriate cell surface distribution of LATs. LATs mediate the transport of amino acids and other molecules such as thyroid hormone. In this respect, CD98hc may also affect development via these transporters.ResultsIn this study, mice were generated from embryonic stem (ES) cell line (PST080) harboring a mutant CD98hc allele (CD98hcΔ/+). Expression of the CD98hc mutant allele results in ΔCD98hc-β geo fusion protein where extracellular C-terminal 102 amino acids of CD98hc are replaced with β geo. Analyses of PST080 ES cells as well as reconstituted frog oocytes demonstrated that ΔCD98hc-β geo fusion protein preserved its ability to interact with integrin β1 although this mutant protein was hardly localized on the cell surface. These findings suggest that ΔCD98hc-β geo protein can mediate integrin signaling but cannot support amino acid transport through LATs. CD98hcΔ/+mice were normal. Although some of the implantation sites lacked embryonic component at E9.5, all the implantation sites contained embryonic component at E7.5. Thus, CD98hcΔ/Δembryos are likely to die between E7.5 and E9.5.ConclusionsConsidering that CD98hc complete knockout (CD98hc-/-) embryos are reported to die shortly after implantation, our findings suggest potential stage-specific roles of CD98hc in murine embryonic development. CD98hc may be essential for early post-implantation development by regulating integrin-dependent signaling, while the other function of CD98hc as a component of amino acid transporters may be required for embryonic development at later stages.