bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new technique for preparation of porous bioceramics with controllable macrostructures
Authors: Zeng Chuisheng , Zhang Jing , Zeng Yanjun , Chen Xiaoming , Yan Yuhua 
Published: November 2009

AbstractThe purpose of this study was to develop a simple and economic method for the preparation of porous bioceramics with controllable macrostructure. Raw materials, including very small organic foam balls as the pore-creating reagent, wax (or paraffin) as the solvent, and oleic acid as the surface active agent, were selected along with bioactive materials such as β-TCP ceramic powder as the main component. The selected components were mixed into a slurry at 30–120ºC and shaped into a green body with a hot die-casting machine at 30–90ºC. The green body was then sintered and porous bioceramics were obtained. The main characteristics of porous bioceramics such as weight loss, compressive strength, connection and size of pores, percolation rate of water, apparent porosity and bulk density were measured. The results indicated that the apparent porosity and the specific surface area were large; the pores were connected in three dimensions and the compressive strength was >1.6 MPa. This study demonstrated that the methods used here are simple and effective in generating porous bioceramics with controllable macrostructures.
Impaired fibrinolysis as a risk factor for Budd-Chiari syndrome
Authors: Hoekstra Jildou , Guimarães Ana H. C. , Leebeek Frank W. G. , Darwish Murad Sarwa , Malfliet Joyce J. M. C. , Plessier Aurelie , Hernandez-Guerra Manuel , Langlet Philippe , Elias Elwyn , Trebicka Jonel , Primignani Massimo , Garcia-Pagan Juan-Carlos , Valla Dominique C. , Rijken Dingeman C. , Janssen Harry L. A. ,   for the European Network for Vascular Disorders of the Liver (EN-Vie)
Published: November 2009

Abstract
In Budd-Chiari syndrome (BCS), thrombosis develops in the hepatic veins or inferior vena cava. To study the relationship between hypofibrinolysis and BCS, we measured plasma levels of fibrinolysis proteins in 101 BCS patients and 101 healthy controls and performed a plasma-based clot lysis assay. In BCS patients, plasminogen activator inhibitor 1 (PAI-1) levels were significantly higher than in controls (median, 6.3 vs 1.4 IU/mL, P < .001). Thrombin-activatable fibrinolysis inhibitor and plasmin inhibitor levels were lower than in controls (13.8 vs 16.9 μg/mL and 0.91 vs 1.02 U/L, both P < .001). Median plasma clot lysis time (CLT) was 73.9 minutes in cases and 73.0 minutes in controls (P = .329). A subgroup of cases displayed clearly elevated CLTs. A CLT above the 90th or 95th percentile of controls was associated with an increased risk of BCS, with odds ratios of 2.4 (95% confidence interval, 1.1-5.5) and 3.4 (95% confidence interval, 1.2-9.7), respectively. In controls, only PAI-1 activity was significantly associated with CLT. Analysis of single nucleotide polymorphisms of fibrinolysis proteins revealed no significant differences between cases and controls. This case-control study provides the first evidence that an impaired fibrinolytic potential, at least partially caused by elevated PAI-1 levels, is related to the presence of BCS.
Eosinophil and T cell markers predict functional decline in COPD patients
Authors: D'Armiento Jeanine M , Scharf Steven M , Roth Michael D , Connett John E , Ghio Andrew , Sternberg David , Goldin Jonathan G , Louis Thomas A , Mao Jenny T , O'Connor George T , Ramsdell Joe W , Ries Andrew L , Schluger Neil W , Sciurba Frank C , Skeans Melissa A , Voelker Helen , Walter Robert E , Wendt Christine H , Weinmann Gail G , Wise Robert A , Foronjy Robert F 
Published: November 2009

AbstractBackgroundThe major marker utilized to monitor COPD patients is forced expiratory volume in one second (FEV1). However, asingle measurement of FEV1 cannot reliably predict subsequent decline. Recent studies indicate that T lymphocytes and eosinophils are important determinants of disease stability in COPD. We therefore measured cytokine levels in the lung lavage fluid and plasma of COPD patients in order to determine if the levels of T cell or eosinophil related cytokines were predictive of the future course of the disease.MethodsBaseline lung lavage and plasma samples were collected from COPD subjects with moderately severe airway obstruction and emphysematous changes on chest CT. The study participants were former smokers who had not had a disease exacerbation within the past six months or used steroids within the past two months. Those subjects who demonstrated stable disease over the following six months (ΔFEV1 % predicted = 4.7 ± 7.2; N = 34) were retrospectively compared with study participants who experienced a rapid decline in lung function (ΔFEV1 % predicted = -16.0 ± 6.0; N = 16) during the same time period and with normal controls (N = 11). Plasma and lung lavage cytokines were measured from clinical samples using the Luminex multiplex kit which enabled the simultaneous measurement of several T cell and eosinophil related cytokines.Results and DiscussionStable COPD participants had significantly higher plasma IL-2 levels compared to participants with rapidly progressive COPD (p = 0.04). In contrast, plasma eotaxin-1 levels were significantly lower in stable COPD subjects compared to normal controls (p < 0.03). In addition, lung lavage eotaxin-1 levels were significantly higher in rapidly progressive COPD participants compared to both normal controls (p < 0.02) and stable COPD participants (p < 0.05).ConclusionThese findings indicate that IL-2 and eotaxin-1 levels may be important markers of disease stability in advanced emphysema patients. Prospective studies will need to confirm whether measuring IL-2 or eotaxin-1 can identify patients at risk for rapid disease progression.
SitesIdentify: a protein functional site prediction tool
Authors: Bray Tracey , Chan Pedro , Bougouffa Salim , Greaves Richard , Doig Andrew J , Warwicker Jim 
Published: November 2009

Abstract

Background
The rate of protein structures being deposited in the Protein Data Bank surpasses the capacity to experimentally characterise them and therefore computational methods to analyse these structures have become increasingly important. Identifying the region of the protein most likely to be involved in function is useful in order to gain information about its potential role. There are many available approaches to predict functional site, but many are not made available via a publicly-accessible application.

Results
Here we present a functional site prediction tool (SitesIdentify), based on combining sequence conservation information with geometry-based cleft identification, that is freely available via a web-server. We have shown that SitesIdentify compares favourably to other functional site prediction tools in a comparison of seven methods on a non-redundant set of 237 enzymes with annotated active sites.

Conclusion
SitesIdentify is able to produce comparable accuracy in predicting functional sites to its closest available counterpart, but in addition achieves improved accuracy for proteins with few characterised homologues. SitesIdentify is available via a webserver at http://www.manchester.ac.uk/bioinformatics/sitesidentify/
The isochore patterns of invertebrate genomes
Authors: Cammarano Rosalia , Costantini Maria , Bernardi Giorgio 
Published: November 2009

Abstract

Background
Previous investigations from our laboratory were largely focused on the genome organization of vertebrates. We showed that these genomes are mosaics of isochores, megabase-size DNA sequences that are fairly homogeneous in base composition yet belong to a small number of families that cover a wide compositional spectrum. A question raised by these results concerned how far back in evolution an isochore organization of the eukaryotic genome arose.

Results
The present investigation deals with the compositional patterns of the invertebrates for which full genome sequences, or at least scaffolds, are available. We found that (i) a mosaic of isochores is the long-range organization of all the genomes that we investigated; (ii) the isochore families from the invertebrate genomes matched the corresponding families of vertebrates in GC levels; (iii) the relative amounts of isochore families were remarkably different for different genomes, except for those from phylogenetically close species, such as the Drosophilids.

Conclusion
This work demonstrates not only that an isochore organization is present in all metazoan genomes analyzed that included Nematodes, Arthropods among Protostomia, Echinoderms and Chordates among Deuterostomia, but also that the isochore families of invertebrates share GC levels with the corresponding families of vertebrates.
Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates
Authors: Betancor Laura , Yim Lucia , Fookes Maria , Martinez Araci , Thomson Nicholas R , Ivens Alasdair , Peters Sarah , Bryant Clare , Algorta Gabriela , Kariuki Samuel , Schelotto Felipe , Maskell Duncan , Dougan Gordon , Chabalgoity Jose A 
Published: November 2009

Abstract

Background

Salmonella enterica serovar Enteritidis (S. Enteritidis) has caused major epidemics of gastrointestinal infection in many different countries. In this study we investigate genome divergence and pathogenic potential in S. Enteritidis isolated before, during and after an epidemic in Uruguay.

Results
266 S. Enteritidis isolates were genotyped using RAPD-PCR and a selection were subjected to PFGE analysis. From these, 29 isolates spanning different periods, genetic profiles and sources of isolation were assayed for their ability to infect human epithelial cells and subjected to comparative genomic hybridization using a Salmonella pan-array and the sequenced strain S. Enteritidis PT4 P125109 as reference. Six other isolates from distant countries were included as external comparators.
Two hundred and thirty three chromosomal genes as well as the virulence plasmid were found as variable among S. Enteritidis isolates. Ten out of the 16 chromosomal regions that varied between different isolates correspond to phage-like regions. The 2 oldest pre-epidemic isolates lack phage SE20 and harbour other phage encoded genes that are absent in the sequenced strain. Besides variation in prophage, we found variation in genes involved in metabolism and bacterial fitness. Five epidemic strains lack the complete Salmonella virulence plasmid. Significantly, strains with indistinguishable genetic patterns still showed major differences in their ability to infect epithelial cells, indicating that the approach used was insufficient to detect the genetic basis of this differential behaviour.

Conclusion
The recent epidemic of S. Enteritidis infection in Uruguay has been driven by the introduction of closely related strains of phage type 4 lineage. Our results confirm previous reports demonstrating a high degree of genetic homogeneity among S. Enteritidis isolates. However, 10 of the regions of variability described here are for the first time reported as being variable in S. Enteritidis. In particular, the oldest pre-epidemic isolates carry phage-associated genetic regions not previously reported in S. Enteritidis. Overall, our results support the view that phages play a crucial role in the generation of genetic diversity in S. Enteritidis and that phage SE20 may be a key marker for the emergence of particular isolates capable of causing epidemics.
Serum immunoglobulin G, M and A response to Cryptosporidium parvum in Cryptosporidium-HIV co-infected patients
Authors: Kaushik Kirti , Khurana Sumeeta , Wanchu Ajay , Malla Nancy 
Published: November 2009

AbstractBackgroundCryptosporidium parvum, the protozoan parasite, causes a significant enteric disease in immunocompromised hosts such as HIV patients. The present study was aimed to compare serum IgG, IgM and IgA responses to crude soluble antigen ofC. parvumin HIV seropositive and seronegative patients co-infected withCryptosporidiumand to correlate the responses with symptomatology.MethodsCryptosporidium parvumspecific serum antibody (IgG, IgM and IgA) responses were assessed by ELISA in 11 HIV seropositiveCryptosporidiumpositive (Group I), 20 HIV seropositiveCryptosporidiumnegative (Group II), 10 HIV seronegativeCryptosporidiumpositive (Group III), 20 HIV seronegativeCryptosporidiumnegative healthy individuals (Group IV) and 25 patients with other parasitic diseases (Group V).ResultsA positive IgG and IgA antibody response was observed in significantly higher number ofCryptosporidiuminfected individuals (Gp I and III) compared toCryptosporidiumun-infected individuals (Gp II, IV and V) irrespective of HIV/immune status. Sensitivity of IgG ELISA in our study was found to be higher as compared to IgM and IgA ELISA. The number of patients with positive IgG, IgM and IgA response was not significantly different in HIV seropositiveCryptosporidiumpositive patients with diarrhoea when compared to patients without diarrhoea and in patients with CD4 counts <200 when compared to patients with CD4 counts >200 cells/μl.ConclusionThe study showed specific serum IgG and IgA production in patients infected withCryptosporidium, both HIV seropositive and seronegative as compared to uninfected subjects suggesting induction ofCryptosporidiumspecific humoral immune response in infected subjects. However, there was no difference in number of patients with positive response in HIV seropositive or seronegative groups indicating that HIV status may not be playing significant role in modulation ofCryptosporidiumspecific antibody responses. The number of patients with positive IgG, IgM and IgA response was not significantly different in patients with or without history of diarrhoea thereby indicating thatCryptosporidiumspecific antibody responses may not be necessarily associated with protection from symptomatology.
Emilin1 gene and essential hypertension: a two-stage association study in northern Han Chinese population
Authors: Shen Chong , Lu Xiangfeng , Li Yun , Zhao Qi , Liu Xiaoli , Hou Liping , Wang Laiyuan , Chen Shufeng , Huang Jianfeng , Gu Dongfeng 
Published: November 2009

Abstract

Background
Elastogenesis of elastic extracellular matrix (ECM) which was recognized as a major component of blood vessels has been believed for a long time to play only a passive role in the dynamic vascular changes of typical hypertension. Emilin1 gene participated in the transcription of ECM's formation and was recognized to modulate links TGF-β maturation to blood pressure homeostasis in animal study. Recently relevant advances urge further researches to investigate the role of Emilin1 gene in regulating TGF-β signals involved in elastogenesis and vascular cell defects of essential hypertension (EH).

Methods
We designed a two-stage case-control study and selected three single nucleotide polymorphisms (SNPs), rs3754734, rs2011616 and rs2304682 from the HapMap database, which covered Emilin1 gene. Totally 2,586 subjects were recruited from the International Collaborative Study of Cardiovascular Disease in Asia (InterASIA). In stage 1, all the three SNPs of the Emilin1 gene were genotyped and tested within a subsample including 503 cases and 490 controls, significant SNPs would enter into stage 2 including 814 cases with hypertension and 779 controls and analyze on the basis of testing total 2,586 subjects.

Results
In stage 1, single locus analyses showed that SNPs rs3754734 and rs2011616 had significant association with EH (P < 0.05). In stage 2, weak association for dominant model were observed by age stratification and odds ratio (ORs) of TG+GG vs. TT of rs3754734 were 0.768 (0.584-1.009), 0.985 (0.735-1.320) and 1.346 (1.003-1.806) in < 50, 50-59 and ≥ 60 years group and ORs of GA+AA vs. GG of rs2011616 were 0.745 (0.568-0.977), 1.013 (0.758-1.353) and 1.437 (1.072-1.926) in < 50, 50-59 and ≥ 60 years group respectively. Accordingly, significant interactions were detected between genotypes of rs3754734 and rs2011616 and age for EH, and ORs were 1.758 (1.180-2.620), P = 0.006 and 1.903 (1.281-2.825), P = 0.001, respectively. Results of haplotypes analysis showed that there weren't any haplotypes associated with EH directly, but the interaction of hap2 (GA) and age-group found to be significant after being adjusted for the covariates, OR was 1.220 (1.031-1.444), P value was 0.020.

Conclusion
Our findings don't support positive association of Emilin1 gene with EH, but the interaction of age and genotype variation of rs3754734 and rs2011616 might increase the risk to hypertension.
Initial activation of EpCAM cleavage viacell-to-cell contact
Authors: Denzel Sabine , Maetzel Dorothea , Mack Brigitte , Eggert Carola , Bärr Gabriele , Gires Olivier 
Published: November 2009

Abstract

Background
Epithelial cell adhesion molecule EpCAM is a transmembrane glycoprotein, which is frequently over-expressed in simple epithelia, progenitors, embryonic and tissue stem cells, carcinoma and cancer-initiating cells. Besides functioning as a homophilic adhesion protein, EpCAM is an oncogenic receptor that requires regulated intramembrane proteolysis for activation of its signal transduction capacity. Upon cleavage, the extracellular domain EpEX is released as a soluble ligand while the intracellular domain EpICD translocates into the cytoplasm and eventually into the nucleus in combination with four-and-a-half LIM domains protein 2 (FHL2) and β-catenin, and drives cell proliferation.

Methods
EpCAM cleavage, induction of the target genes, and transmission of proliferation signals were investigated under varying density conditions using confocal laser scanning microscopy, immunoblotting, cell counting, and conditional cell systems.

Results
EpCAM cleavage, induction of the target genes, and transmission of proliferation signals were dependent on adequate cell-to-cell contact. If cell-to-cell contact was prohibited EpCAM did not provide growth advantages. If cells were allowed to undergo contact to each other, EpCAM transmitted proliferation signals based on signal transduction-related cleavage processes. Accordingly, the pre-cleaved version EpICD was not dependent on cell-to-cell contact in order to induce c-myc and cell proliferation, but necessitated nuclear translocation. For the case of contact-inhibited cells, although cleavage of EpCAM occurred, nuclear translocation of EpICD was reduced, as were EpCAM effects.

Conclusion
Activation of EpCAM's cleavage and oncogenic capacity is dependent on cellular interaction (juxtacrine) to provide for initial signals of regulated intramembrane proteolysis, which then support signalling via soluble EpEX (paracrine).
A sex-role-preference model for HIV transmission among men who have sex with men in China
Authors: Lou Jie , Wu Jianhong , Chen Li , Ruan Yuhua , Shao Yiming 
Published: November 2009

Abstract

Background
Men who have sex with men (MSM) are much more likely to be infected with HIV than the general population. China has a sizable population of MSM, including gay, bisexual men, money boys and some rural workers. So reducing HIV infection in this population is an important component of the national HIV/AIDS prevention and control program.

Methods
We develop a mathematical model using a sex-role-preference framework to predict HIV infection in the MSM population and to evaluate different intervention strategies.

Results
An analytic formula for the basic reproduction ratio R
0 was obtained; this yields R
0 = 3.9296 in the current situation, so HIV will spread very fast in the MSM population if no intervention measure is implemented in a timely fashion. The persistence of HIV infection and the existence of disease equilibrium (or equilibria) are also shown. We utilized our model to simulate possible outcomes of antiretroviral therapy and vaccination for the MSM population. We compared the effects of these intervention measures under different assumptions about MSM behaviour. We also found that R
0 is a decreasing function of the death rate of HIV-infected individuals, following a power law at least asymptotically.

Conclusion
HIV will spread very fast in the MSM population unless intervention measures are implemented urgently. Antiretroviral therapy can have substantial impact on the reduction of HIV among the MSM population, even if disinhibition is considered. The effect of protected sexual behaviour on controlling the epidemic in the MSM population largely depends on the sex-ratio preference of different sub-populations.
CD 9 and vimentin distinguish clear cell from chromophobe renal cell carcinoma
Authors: Williams Ariel A , Higgins John PT , Zhao Hongjuan , Ljungberg Börje , Brooks James D 
Published: November 2009

Abstract

Background
Clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) can usually be distinguished by histologic characteristics. Occasionally, diagnosis proves challenging and diagnostic difficulty will likely increase as needle biopsies of renal lesions become more common.

Methods
To identify markers that aid in differentiating ccRCC from chRCC, we used gene expression profiles to identify candidate markers that correlate with histology. 39 antisera and antibodies, including 35 for transcripts identified from gene expression profiling, were evaluated. Promising markers were tested on a tissue microarray (TMA) containing 428 renal neoplasms. Strength of staining of each core on the TMA was formally scored and the distribution of staining across different types of renal neoplasms was analyzed.

Results
Based on results from initial immunohistochemical staining of multitissue titer arrays, 23 of the antisera and antibodies were selected for staining of the TMA. For 7 of these markers, strength of staining of each core on the TMA was formally scored. Vimentin (positive in ccRCC) and CD9 (positive in chRCC) best distinguished ccRCC from chRCC. The combination of vimentin negativity and CD9 positivity was found to distinguish chRCC from ccRCC with a sensitivity of 100.0% and a specificity of 95.2%.

Conclusion
Based on gene expression analysis, we identify CD9 and vimentin as candidate markers for distinguishing between ccRCC and chRCC. In difficult cases and particularly when the amount of diagnostic tissue is limited, vimentin and CD9 staining could serve as a useful adjunct in the differential diagnosis of ccRCC and chRCC.