bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical characteristics of Pneumocystis pneumonia in non-HIV patients and prognostic factors including microbiological genotypes
Authors: Matsumura Yasufumi , Shindo Yuichiro , Iinuma Yoshitsugu , Yamamoto Masaki , Shirano Michinori , Matsushima Aki , Nagao Miki , Ito Yutaka , Takakura Shunji , Hasegawa Yoshinori , Ichiyama Satoshi 
Published: April 2011

Abstract

Background
The number of patients with non-HIV Pneumocystis pneumonia (PCP) is increasing with widespread immunosuppressive treatment. We investigated the clinical characteristics of non-HIV PCP and its association with microbiological genotypes.

Methods
Between January 2005 and March 2010, all patients in 2 university hospitals who had been diagnosed with PCP by PCR were enrolled in this study. Retrospective chart review of patients, microbiological genotypes, and association with 30-day mortality were examined.

Results
Of the 82 adult patients investigated, 50 patients (61%) had inflammatory diseases, 17 (21%) had solid malignancies, 12 (15%) had hematological malignancies, and 6 (7%) had received transplantations. All patients received immunosuppressive agents or antitumor chemotherapeutic drugs. Plasma (1→3) β-D-glucan levels were elevated in 80% of patients, and were significantly reduced after treatment in both survivors and non-survivors. However, β-D-glucan increased in 18% of survivors and was normal in only 33% after treatment. Concomitant invasive pulmonary aspergillosis was detected in 5 patients. Fifty-six respiratory samples were stored for genotyping. A dihydropteroate synthase mutation associated with trimethoprim-sulfamethoxazole resistance was found in only 1 of the 53 patients. The most prevalent genotype of mitochondrial large-subunit rRNA was genotype 1, followed by genotype 4. The most prevalent genotype of internal transcribed spacers of the nuclear rRNA operon was Eb, followed by Eg and Bi. Thirty-day mortality was 24%, in which logistic regression analysis revealed association with serum albumin and mechanical ventilation, but no association with genotypes.

Conclusions
In non-HIV PCP, poorer general and respiratory conditions at diagnosis were independent predictors of mortality. β-D-glucan may not be useful for monitoring the response to treatment, and genotypes were not associated with mortality.
Human PTCHD3 nulls: rare copy number and sequence variants suggest a non-essential gene
Authors: Ghahramani Seno Mohammad M , Kwan Benjamin YM , Lee-Ng Ka Ki M , Moessner Rainald , Lionel Anath C , Marshall Christian R , Scherer Stephen W 
Published: April 2011

Abstract

Background
Copy number variations (CNVs) can contribute to variable degrees of fitness and/or disease predisposition. Recent studies show that at least 1% of any given genome is copy number variable when compared to the human reference sequence assembly. Homozygous deletions (or CNV nulls) that are found in the normal population are of particular interest because they may serve to define non-essential genes in human biology.

Results
In a genomic screen investigating CNV in Autism Spectrum Disorders (ASDs) we detected a heterozygous deletion on chromosome 10p12.1, spanning the Patched-domain containing 3 (PTCHD3) gene, at a frequency of ~1.4% (6/427). This finding seemed interesting, given recent discoveries on the role of another Patched-domain containing gene (PTCHD1) in ASD. Screening of another 177 ASD probands yielded two additional heterozygous deletions bringing the frequency to 1.3% (8/604). The deletion was found at a frequency of ~0.73% (27/3,695) in combined control population from North America and Northern Europe predominately of European ancestry. Screening of the human genome diversity panel (HGDP-CEPH) covering worldwide populations yielded deletions in 7/1,043 unrelated individuals and those detected were confined to individuals of European/Mediterranean/Middle Eastern ancestry. Breakpoint mapping yielded an identical 102,624 bp deletion in all cases and controls tested, suggesting a common ancestral event. Interestingly, this CNV occurs at a break of synteny between humans and mouse. Considering all data, however, no significant association of these rare PTCHD3 deletions with ASD was observed. Notwithstanding, our RNA expression studies detected PTCHD3 in several tissues, and a novel shorter isoform for PTCHD3 was characterized. Expression in transfected COS-7 cells showed PTCHD3 isoforms colocalize with calnexin in the endoplasmic reticulum. The presence of a patched (Ptc) domain suggested a role for PTCHD3 in various biological processes mediated through the Hedgehog (Hh) signaling pathway. However, further investigation yielded one individual harboring a homozygous deletion (PTCHD3 null) without ASD or any other overt abnormal phenotype. Exon sequencing of PTCHD3 in other individuals with deletions revealed compound point mutations also resulting in a null state.

Conclusion
Our data suggests that PTCHD3 may be a non-essential gene in some humans and characterization of this novel CNV at 10p12.1 will facilitate population and disease studies.
Interaction and uptake of exosomes by ovarian cancer cells
Authors: Escrevente Cristina , Keller Sascha , Altevogt Peter , Costa Júlia 
Published: April 2011

Abstract

Background
Exosomes consist of membrane vesicles that are secreted by several cell types, including tumors and have been found in biological fluids. Exosomes interact with other cells and may serve as vehicles for the transfer of protein and RNA among cells.

Methods
SKOV3 exosomes were labelled with carboxyfluoresceine diacetate succinimidyl-ester and collected by ultracentrifugation. Uptake of these vesicles, under different conditions, by the same cells from where they originated was monitored by immunofluorescence microscopy and flow cytometry analysis. Lectin analysis was performed to investigate the glycosylation properties of proteins from exosomes and cellular extracts.

Results
In this work, the ovarian carcinoma SKOV3 cell line has been shown to internalize exosomes from the same cells via several endocytic pathways that were strongly inhibited at 4°C, indicating their energy dependence. Partial colocalization with the endosome marker EEA1 and inhibition by chlorpromazine suggested the involvement of clathrin-dependent endocytosis. Furthermore, uptake inhibition in the presence of 5-ethyl-N-isopropyl amiloride, cytochalasin D and methyl-beta-cyclodextrin suggested the involvement of additional endocytic pathways. The uptake required proteins from the exosomes and from the cells since it was inhibited after proteinase K treatments. The exosomes were found to be enriched in specific mannose- and sialic acid-containing glycoproteins. Sialic acid removal caused a small but non-significant increase in uptake. Furthermore, the monosaccharides D-galactose, α-L-fucose, α-D-mannose, D-N-acetylglucosamine and the disaccharide β-lactose reduced exosomes uptake to a comparable extent as the control D-glucose.

Conclusions
In conclusion, exosomes are internalized by ovarian tumor cells via various endocytic pathways and proteins from exosomes and cells are required for uptake. On the other hand, exosomes are enriched in specific glycoproteins that may constitute exosome markers. This work contributes to the knowledge about the properties and dynamics of exosomes in cancer.
Replicase-based plasmid DNA shows anti-tumor activity
Authors: Rodriguez B Leticia , Yu Zhen , Chung Woon-Gye , Weiss Richard , Cui Zhengrong 
Published: April 2011

Abstract

Background
Double stranded RNA (dsRNA) has multiple anti-tumor mechanisms. Over the past several decades, there have been numerous attempts to utilize synthetic dsRNA to control tumor growth in animal models and clinical trials. Recently, it became clear that intracellular dsRNA is more effective than extracellular dsRNA on promoting apoptosis and orchestrating adaptive immune responses. To overcome the difficulty in delivering a large dose of synthetic dsRNA into tumors, we propose to deliver a RNA replicase-based plasmid DNA, hypothesizing that the dsRNA generated by the replicase-based plasmid in tumor cells will inhibit tumor growth.

Methods
The anti-tumor activity of a plasmid (pSIN-β) that encodes the sindbis RNA replicase genes (nsp1-4) was evaluated in mice with model tumors (TC-1 lung cancer cells or B16 melanoma cells) and compared to a traditional pCMV-β plasmid.

Results
In cell culture, transfection of tumor cells with pSIN-β generated dsRNA. In mice with model tumors, pSIN-β more effectively delayed tumor growth than pCMV-β, and in some cases, eradicated the tumors.

Conclusion
RNA replicase-based plasmid may be exploited to generate intracellular dsRNA to control tumor growth.
Number of casual male sexual partners and associated factors among men who have sex with men: Results from the National HIV Behavioral Surveillance system
Authors: Rosenberg Eli S , Sullivan Patrick S , DiNenno Elizabeth A , Salazar Laura F , Sanchez Travis H 
Published: April 2011

Abstract

Background
In 2006, the majority of new HIV infections were in MSM. We sought to describe numbers of casual sex partners among US MSM.

Methods
Data are from the first MSM cycle of the National HIV Behavioral Surveillance system, conducted from 2003 to 2005. Relationships between number of casual male sex partners within the previous year and demographic information, self-reported HIV status, and risk behaviors were determined through regression models.

Results
Among 11,191 sexually active MSM, 76% reported a casual male partner. The median casual partner number was three. Lower number of casual partners was associated with black race, Hispanic ethnicity, and having a main sex partner in the previous year. Factors associated with a higher number included gay identity, exchange sex, both injection and non-injection drug use. Being HIV-positive was associated with more partners among non-blacks only. Age differences in partner number were seen only among chat room users.

Conclusions
MSM who were black, Hispanic or had a main sex partner reported fewer casual sex partners. Our results suggest specific populations of MSM who may benefit most from interventions to reduce casual partner numbers.
The effect of health insurance reform on the number of cataract surgeries in Chongqing, China
Authors: Chen Xiaofan , Chen Chunlin , Zhang Yao , Yuan Rongdi , YE Jian 
Published: April 2011

Abstract

Background
Cataracts are the leading cause of blindness in China, and poverty is a major barrier to having cataract surgery. In 2003, the Chinese government began a series of new national health insurance reforms, including the New Cooperative Medical Scheme (NCMS) and the Urban Resident Basic Health Insurance scheme (URBMI). These two programs, combined with the previously existing Urban Employee Basic Health Insurance (UEBMI) program, aimed to make it easier for individuals to receive medical treatment. This study reports cataract surgery numbers in rural and urban populations and the proportion of these who had health insurance in Chongqing, China from 2003 to 2008.

Methods
The medical records of a consecutive case series, including 14,700 eyes of 13,262 patients who underwent age-related cataract surgery in eight hospitals in Chongqing from January 1, 2003, to December 31, 2008, were analysed retrospectively via multi-stage cluster sampling.

Results
In the past six years, the total number of cataract surgeries had increased each year as had the number of patients with insurance. Both the number of surgeries and the number of insured patients were much higher in the urban group than in the rural group. The rate of increase in the rural group however was much higher than in the urban group, especially in 2007 and 2008. The odds ratios of having health insurance for urban vs. rural individuals were relatively stable from 2003 to 2006, but it decreased in 2007 and was significantly lower in 2008.

Conclusions
Health insurance appears to be an important factor associated with increased cataract surgery in Chongqing, China. With the implementation of health insurance, the number of Chongqing's cataract surgeries was increased year by year.
Comparative analysis of remotely-sensed data products via ecological niche modeling of avian influenza case occurrences in Middle Eastern poultry
Authors: Bodbyl-Roels Sarah , Peterson ATownsend , Xiao Xiangming 
Published: April 2011

Abstract

Background
Ecological niche modeling integrates known sites of occurrence of species or phenomena with data on environmental variation across landscapes to infer environmental spaces potentially inhabited (i.e., the ecological niche) to generate predictive maps of potential distributions in geographic space. Key inputs to this process include raster data layers characterizing spatial variation in environmental parameters, such as vegetation indices from remotely sensed satellite imagery. The extent to which ecological niche models reflect real-world distributions depends on a number of factors, but an obvious concern is the quality and content of the environmental data layers.

Methods
We assessed ecological niche model predictions of H5N1 avian flu presence quantitatively within and among four geographic regions, based on models incorporating two means of summarizing three vegetation indices derived from the MODIS satellite. We evaluated our models for predictive ability using partial ROC analysis and GLM ANOVA to compare performance among indices and regions.

Results
We found correlations between vegetation indices to be high, such that they contain information that overlaps broadly. Neither the type of vegetation index used nor method of summary affected model performance significantly. However, the degree to which model predictions had to be transferred (i.e., projected onto landscapes and conditions not represented on the landscape of training) impacted predictive strength greatly (within-region model predictions far out-performed models projected among regions).

Conclusion
Our results provide the first quantitative tests of most appropriate uses of different remotely sensed data sets in ecological niche modeling applications. While our testing did not result in a decisive "best" index product or means of summarizing indices, it emphasizes the need for careful evaluation of products used in modeling (e.g. matching temporal dimensions and spatial resolution) for optimum performance, instead of simple reliance on large numbers of data layers.
Evidence of fibrinogen as a target of citrullination in IgM rheumatoid factor-positive polyarticular juvenile idiopathic arthritis
Authors: Gilliam Brooke E , Reed Melinda R , Chauhan Anil K , Dehlendorf Amanda B , Moore Terry L 
Published: April 2011

Abstract

Background
Several studies have noted the significance of measuring anti-cyclic citrullinated peptide (CCP) antibodies in juvenile idiopathic arthritis (JIA) as an important indicator for destructive disease, as is the case in rheumatoid arthritis (RA). While the role of anti-CCP antibodies in RA and JIA has become better understood, the identity of the target proteins of this modification has remained elusive. In this study, we evaluated serum from patients with various subtypes of JIA to investigate the presence of anti-deiminated (citrullinated) fibrinogen and anti-citrullinated α-enolase antibodies, and their association with RF and anti-CCP antibody isotypes.

Methods
Sera were obtained from 96 JIA patients, 19 systemic lupus erythematosus (SLE) patients, and 10 healthy children. All sera were measured for antibodies against citrullinated and native fibrinogen and α-enolase by an enzyme linked immunosorbent assay (ELISA). In addition, all sera were assayed for anti-CCP antibody isotypes and rheumatoid factor (RF) isotypes by ELISA. The relationship between anti-citrullinated fibrinogen and anti-α-enolase antibodies and disease activity and joint damage were also investigated. All results were correlated with clinical and laboratory parameters using Spearman's rho correlation coefficient. Multiple logistic regression analysis was utilized to identify which variables were associated with joint erosions and diagnosis of JIA.

Results
Thirty-one JIA patients (32%) demonstrated reactivity to citrullinated fibrinogen and 9 (9%) to citrullinated α-enolase. Reactivity to citrullinated fibrinogen and α-enolase was predominantly found in IgM RF-positive polyarthritis patients. Fourteen JIA patients reacted with native α-enolase and a higher percentage of SLE patients reacted with citrullinated α-enolase when compared to JIA patients. Anti-citrullinated fibrinogen antibodies correlated with the presence of IgG anti-CCP antibodies and IgA and IgM RF. The presence of anti-citrullinated α-enolase antibodies correlated with IgA anti-CCP antibodies. IgG anti-CCP antibodies were significantly associated with joint damage and anti-citrullinated fibrinogen antibodies were strongly associated with JIA when compared to control groups. Anti-citrullinated fibrinogen antibodies demonstrated high sensitivity (81%) for IgM RF-positive polyarticular JIA. IgG anti-CCP antibodies had the highest specificity (95%) for JIA, with anti-citrullinated fibrinogen antibodies, IgA anti-CCP antibodies and IgA RF all following at 84%.

Conclusions
JIA patient sera exhibited strong reactivity to anti-citrullinated fibrinogen antibodies and demonstrated high sensitivity and specificity for JIA, primarily in IgM RF-positive polyarthritis patients. Fibrinogen is one of several protein targets for citrullination in JIA.
Round-robin test on thermal conductivity measurement of ZnO nanofluids and comparison of experimental results with theoretical bounds
Authors: Lee Wook-Hyun , Rhee Chang-Kyu , Koo Junemo , Lee Jaekeun , Jang Seok Pil , Choi Stephen US , Lee Ki-Woong , Bae Hwa-Young , Lee Gyoung-Ja , Kim Chang-Kyu , Hong Sung Wook , Kwon Younghwan , Kim Doohyun , Kim Soo Hyung , Hwang Kyo Sik , Kim Hyun Jin , Ha Hyo Jun , Lee Seung-Hyun , Choi Chul Jin , Lee Ji-Hwan 
Published: April 2011

AbstractEthylene glycol (EG)-based zinc oxide (ZnO) nanofluids containing no surfactant have been manufactured by one-step pulsed wire evaporation (PWE) method. Round-robin tests on thermal conductivity measurements of three samples of EG-based ZnO nanofluids have been conducted by five participating labs, four using accurate measurement apparatuses developed in house and one using a commercial device. The results have been compared with several theoretical bounds on the effective thermal conductivity of heterogeneous systems. This study convincingly demonstrates that the large enhancements in the thermal conductivities of EG-based ZnO nanofluids tested are beyond the lower and upper bounds calculated using the models of the Maxwell and Nan et al. with and without the interfacial thermal resistance.
Gold-ionic liquid nanofluids with preferably tribological properties and thermal conductivity
Authors: Wang Baogang , Wang Xiaobo , Lou Wenjing , Hao Jingcheng 
Published: April 2011

AbstractGold/1-butyl-3-methylimidazolium hexafluorophosphate (Au/[Bmim][PF6]) nanofluids containing different stabilizing agents were fabricated by a facile one-step chemical reduction method, of which the nanofluids stabilized by cetyltrimethylammonium bromide (CTABr) exhibited ultrahighly thermodynamic stability. The transmission electron microscopy, UV-visible absorption, Fourier transform infrared, and X-ray photoelectron characterizations were conducted to reveal the stable mechanism. Then, the tribological properties of these ionic liquid (IL)-based gold nanofluids were first investigated in more detail. In comparison with pure [Bmim][PF6] and the nanofluids possessing poor stability, the nanofluids with high stability exhibited much better friction-reduction and anti-wear properties. For instance, the friction coefficient and wear volume lubricated by the nanofluid with rather low volumetric concentration (1.02 × 10-3%) stabilized by CTABr under 800 N are 13.8 and 45.4% lower than that of pure [Bmim][PF6], confirming that soft Au nanoparticles (Au NPs) also can be excellent additives for high performance lubricants especially under high loads. Moreover, the thermal conductivity (TC) of the stable nanofluids with three volumetric fraction (2.55 × 10-4, 5.1 × 10-4, and 1.02 × 10-3%) was also measured by a transient hot wire method as a function of temperature (33 to 81°C). The results indicate that the TC of the nanofluid (1.02 × 10-3%) is 13.1% higher than that of [Bmim][PF6] at 81°C but no obvious variation at 33°C. The conspicuously temperature-dependent and greatly enhanced TC of Au/[Bmim][PF6] nanofluids stabilized by CTABr could be attributed to micro-convection caused by the Brownian motion of Au NPs. Our results should open new avenues to utilize Au NPs and ILs in tribology and the high-temperature heat transfer field.
Gallium hydride vapor phase epitaxy of GaN nanowires
Authors: Zervos Matthew , Othonos Andreas 
Published: April 2011

AbstractStraight GaN nanowires (NWs) with diameters of 50 nm, lengths up to 10 μm and a hexagonal wurtzite crystal structure have been grown at 900°C on 0.5 nm Au/Si(001) via the reaction of Ga with NH3 and N2:H2, where the H2 content was varied between 10 and 100%. The growth of high-quality GaN NWs depends critically on the thickness of Au and Ga vapor pressure while no deposition occurs on plain Si(001). Increasing the H2 content leads to an increase in the growth rate, a reduction in the areal density of the GaN NWs and a suppression of the underlying amorphous (α)-like GaN layer which occurs without H2. The increase in growth rate with H2 content is a direct consequence of the reaction of Ga with H2 which leads to the formation of Ga hydride that reacts efficiently with NH3 at the top of the GaN NWs. Moreover, the reduction in the areal density of the GaN NWs and suppression of the α-like GaN layer is attributed to the reaction of H2 with Ga in the immediate vicinity of the Au NPs. Finally, the incorporation of H2 leads to a significant improvement in the near band edge photoluminescence through a suppression of the non-radiative recombination via surface states which become passivated not only via H2, but also via a reduction of O2-related defects.
Fabrication and evolution of multilayer silver nanofilms for surface-enhanced Raman scattering sensing of arsenate
Authors: Hao Jumin , Han Mei-Juan , Xu Zhonghou , Li Jinwei , Meng Xiaoguang 
Published: April 2011

AbstractSurface-enhanced Raman scattering (SERS) has recently been investigated extensively for chemical and biomolecular sensing. Multilayer silver (Ag) nanofilms deposited on glass slides by a simple electroless deposition process have been fabricated as active substrates (Ag/GL substrates) for arsenate SERS sensing. The nanostructures and layer characteristics of the multilayer Ag films could be tuned by varying the concentrations of reactants (AgNO3/BuNH2) and reaction time. A Ag nanoparticles (AgNPs) double-layer was formed by directly reducing Ag+ ions on the glass surfaces, while a top layer (3rd-layer) of Ag dendrites was deposited on the double-layer by self-assembling AgNPs or AgNPs aggregates which had already formed in the suspension. The SERS spectra of arsenate showed that characteristic SERS bands of arsenate appear at approximately 780 and 420 cm-1, and the former possesses higher SERS intensity. By comparing the peak heights of the approximately 780 cm-1 band of the SERS spectra, the optimal Ag/GL substrate has been obtained for the most sensitive SERS sensing of arsenate. Using this optimal substrate, the limit of detection (LOD) of arsenate was determined to be approximately 5 μg·l-1.