bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thyroid stimulating hormone, independent of thyroid hormone, can elevate the serum total cholesterol level in patients with coronary heart disease: a cross-sectional design
Authors: Xu Chao , Yang Xiaomei , Liu Wenhui , Yuan Haitao , Yu Chunxiao , Gao Ling , Zhao Jiajun 
Published: June 2012

Abstract

Background
The relationship between TSH and the lipid profile is contradictory because few studies have excluded the potential influence of the thyroid hormones (TH). The aim of the present study was to evaluate the relationship between serum TSH levels and the lipid profile independent of TH.

Methods
1302 CHD patients diagnosed by coronary angiography were retrospectively studied. The prevalence and distribution of thyroid dysfunction were analyzed first. To assess the impact of TSH on serum lipids, Pearson’s correlation analysis was performed after adjustments for classic factors and TH. To calculate the extent of the effect of TSH on the serum cholesterol level, the partial least squares method and additional statistical methods were used.

Results
After the exclusions, a total of 568 patients (270 males and 298 females with a mean age of 63.56 ± 11.376 years) were selected. The prevalence of thyroid dysfunction among the patients was 18.66%, and the prevalence of hypothyroidism (15.32%) was higher than that of hyperthyroidism (3.34%). Even after adjusting for confounding factors, such as sex, age, smoking status, fasting plasma glucose levels and TH, a significant positive impact of TSH on the serum total cholesterol (TC) level was revealed (r = 0.095, p = 0.036). Each 1 mIU/L increase in the TSH level might be linked to a 0.015580712 mmol/L elevation of the serum TC value.

Conclusions
TSH can increase the TC level in CHD patients independent of TH. The present study suggests a potential physiological role of TSH and the importance of maintaining an appropriate TSH level in CHD patients.
Transcriptome-based identification of antioxidative gene expression after fish oil supplementation in normo- and dyslipidemic men
Authors: Schmidt Simone , Stahl Frank , Mutz Kai-Oliver , Scheper Thomas , Hahn Andreas , Schuchardt Jan Philipp 
Published: June 2012

AbstractBackgroundThe beneficial effects of omega-3 polyunsaturated fatty acids (n-3 PUFAs), especially in dyslipidemic subjects with a high risk of cardiovascular disease, are widely described in the literature. A lot of effects of n-3 PUFAs and their oxidized metabolites are triggered by regulating the expression of genes. Currently, it is uncertain if the administration of n-3 PUFAs results in different expression changes of genes related to antioxidative mechanisms in normo- and dyslipidemic subjects, which may partly explain their cardioprotective effects. The aim of this study was to investigate the effects of n-3 PUFA supplementation on expression changes of genes involved in oxidative processes.MethodsTen normo- and ten dyslipidemic men were supplemented for twelve weeks with fish oil capsules, providing 1.14 g docosahexaenoic acid and 1.56 g eicosapentaenoic acid. Gene expression levels were determined by whole genome microarray analysis and quantitative real-time polymerase chain reaction (qRT-PCR).ResultsUsing microarrays, we discovered an increased expression of antioxidative enzymes and a decreased expression of pro-oxidative and tissue enzymes, such as cytochrome P450 enzymes and matrix metalloproteinases, in both normo- and dyslipidemic men. An up-regulation of catalase and heme oxigenase 2 in both normo- and dyslipidemic subjects and an up-regulation of cytochrome P450 enzyme 1A2 only in dyslipidemic subjects could be observed by qRT-PCR analysis.ConclusionsSupplementation of normo- and dyslipidemic subjects with n-3 PUFAs changed the expression of genes related to oxidative processes, which may suggest antioxidative and potential cardioprotective effects of n-3 PUFAs. Further studies combining genetic and metabolic endpoints are needed to verify the regulative effects of n-3 PUFAs in antioxidative gene expression to better understand their beneficial effects in health and disease prevention.Trial registrationClinicalTrials.gov (ID: NCT01089231)
The influence of corneal astigmatism on retinal nerve fiber layer thickness and optic nerve head parameter measurements by spectral-domain optical coherence tomography
Authors: Liu Lin , Zou Jun , Huang Hui , Yang Jian-guo , Chen Shao-rong 
Published: June 2012

Abstract

Background
To evaluate the influence of corneal astigmatism (CA) on retinal nerve fiber layer (RNFL) thickness and optic nerve head(ONH) parameters measured with spectral-domain optical coherence tomography (OCT) in high myopes patients before refractive surgery.

Methods
Seventy eyes of 35 consecutive refractive surgery candidates were included in this study. The mean age of the subjects was 26.42 ± 6.95 years, the average CA was −1.17 diopters (D; SD 0.64; range −0.2 to-3.3D), All subjects in this study were WTR CA. 34 eyes were in the normal CA group with a mean CA was −0.67 ± 0.28D, 36 eyes were in the high CA group with an average CA of −1.65 ± 0.49D. All subjects underwent ophthalmic examination and imaging with the Cirrus HD OCT.

Results
No significant difference was noted in the average cup-to-disk ratio, vertical cup-to-disk ratio and cup volume (all P values > 0.05). Compared with the normal CA group, the high CA group had a larger disc area and rim area, thinner RNFL thickness in the temporal quadrant, and the superotemporal and inferotemporal peaks were farther to the temporal horizon (All P values < 0.05). There were no significant differences between the two groups in global average RNFL thickness, as well as superior, nasal and inferior quadrant RNFL thickness (all P values > 0.05).

Conclusions
The degree of with-the-rule CA should be considered when interpreting ONH parameters and peripapillary RNFL thickness measured by the Cirrus HD OCT.

Virtual slides
The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/1148475676881895
The clinicopathologic association of c-MET overexpression in Iranian gastric carcinomas; an immunohistochemical study of tissue microarrays
Authors: Sotoudeh Kambiz , Hashemi Forough , Madjd Zahra , Sadeghipour Alireza , Molanaei Saadat , Kalantary Elham 
Published: June 2012

Abstract

Background
c-MET is an oncogene protein that plays important role in gastric carcinogenesis and has been introduced as a prognostic marker and potential therapeutic target. The aim of this study was to evaluate the frequency of c-MET overexpression and its relationship with clinicopathological variables in gastric cancer of Iranian population using tissue microarray.

Methods
In a cross sectional study, representative paraffin blocks of 130 patients with gastric carcinoma treated by curative gastrectomy during a 2 years period of 2008–2009 in two university hospitals in Tehran-Iran were collected in tissue microarray and c-MET expression was studied by immunohistochemical staining.

Results
Finally 124 cases were evaluated, constituted of 99 male and 25 female with the average age of 61.5 years. In 71% (88/124) of tumors, c-MET high expression was found. c-MET high expression was more associated with intestinal than diffuse tumor type (P = 0.04), deeper tumor invasion, pT3 and pT4 versus pT1 and pT2 (P = 0.014), neural invasion (P = 0.002) and advanced TNM staging, stage 3 and 4 versus stage 1 and2 (P = 0.044). The c-MET high expression was not associated with age, sex, tumor location, differentiation grade and distant metastasis, but relative associations with lymph node metastasis (P = 0.065) and vascular invasion (P = 0.078) were observed.

Conclusions
c-MET oncogene protein was frequently overexpressed in Iranian gastric carcinomas and it was related to clinicopathological characteristics such as tumor type, depth of invasion, neural invasion and TNM staging. It can also support the idea that c-MET is a potential marker for target therapy in Iranian gastric cancer.

Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9744598757151429
Evaluating observer agreement of scoring systems for foot integrity and footrot lesions in sheep
Authors: Foddai Alessandro , Green Laura E , Mason Sam A , Kaler Jasmeet 
Published: June 2012

AbstractBackgroundA scoring scale with five ordinal categories is used for visual diagnosis of footrot in sheep and to study its epidemiology and control. More recently a 4 point ordinal scale has been used by researchers to score foot integrity (wall and sole horn damage) in sheep. There is no information on observer agreement using either of these scales. Observer agreement for ordinal scores is usually estimated by single measure values such as weighted kappa or Kendall’s coefficient of concordance which provide no information where the disagreement lies. Modeling techniques such as latent class models provide information on both observer bias and whether observers have different thresholds at which they change the score given. In this paper we use weighted kappa and located latent class modeling to explore observer agreement when scoring footrot lesions (using photographs and videos) and foot integrity (using post mortem specimens) in sheep. We used 3 observers and 80 photographs and videos and 80 feet respectively.ResultsBoth footrot and foot integrity scoring scales were more consistent within observers than between. The weighted kappa values between observers for both footrot and integrity scoring scales ranged from moderate to substantial. There was disagreement between observers with both observer bias and different thresholds between score values. The between observer thresholds were different for scores 1 and 2 for footrot (using photographs and videos) and for all scores for integrity (both walls and soles). The within observer agreement was higher with weighted kappa values ranging from substantial to almost perfect. Within observer thresholds were also more consistent than between observer thresholds. Scoring using photographs was less variable than scoring using video clips or feet.ConclusionsLatent class modeling is a useful method for exploring components of disagreement within and between observers and this information could be used when developing a scoring system to improve reliability.
Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments
Authors: Ramirez-Gonzalez Ricardo H , Bonnal Raoul , Caccamo Mario , MacLean Daniel 
Published: June 2012

Abstract

Background
The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities are implemented in C and provide an API for programmatic access, to help make this functionality available to programmers wishing to develop in the high level Ruby language we have developed bio-samtools, a Ruby binding to the SAMtools library.

Results
The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned.

Conclusions
Bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access information in the popular and common SAM/BAM format.
Fermentative hydrogen production from glucose and starch using pure strains and artificial co-cultures of Clostridium spp.
Authors: Masset Julien , Calusinska Magdalena , Hamilton Christopher , Hiligsmann Serge , Joris Bernard , Wilmotte Annick , Thonart Philippe 
Published: June 2012

AbstractBackgroundPure bacterial strains give better yields when producing H2than mixed, natural communities. However the main drawback with the pure cultures is the need to perform the fermentations under sterile conditions. Therefore, H2production using artificial co-cultures, composed of well characterized strains, is one of the directions currently undertaken in the field of biohydrogen research.ResultsFour pureClostridiumcultures, includingC. butyricumCWBI1009,C. pasteurianumDSM525,C. beijerinckiiDSM1820 andC. felsineumDSM749, and three different co-cultures composed of (1)C. pasteurianumand C.felsineum, (2)C. butyricumandC. felsineum, (3)C. butyricumandC. pasteurianum, were grown in 20 L batch bioreactors. In the first part of the study a strategy composed of three-culture sequences was developed to determine the optimal pH for H2production (sequence 1); and the H2-producing potential of each pure strain and co-culture, during glucose (sequence 2) and starch (sequence 3) fermentations at the optimal pH. The best H2yields were obtained for starch fermentations, and the highest yield of 2.91 mol H2/ mol hexose was reported forC. butyricum. By contrast, the biogas production rates were higher for glucose fermentations and the highest value of 1.5 L biogas/ h was observed for the co-culture (1). In general co-cultures produced H2at higher rates than the pureClostridiumcultures, without negatively affecting the H2yields. Interestingly, all theClostridiumstrains and co-cultures were shown to utilize lactate (present in a starch-containing medium), andC. beijerinckiiwas able to re-consume formate producing additional H2. In the second part of the study the co-culture (3) was used to produce H2during 13 days of glucose fermentation in a sequencing batch reactor (SBR). In addition, the species dynamics, as monitored by qPCR (quantitative real-time PCR), showed a stable coexistence ofC. pasteurianumandC. butyricumduring this fermentation.ConclusionsThe four pureClostridiumstrains and the artificial co-cultures tested in this study were shown to efficiently produce H2using glucose and starch as carbon sources. The artificial co-cultures produced H2at higher rates than the pure strains, while the H2yields were only slightly affected.
Differential expression of breast cancer-associated genes between stage- and age-matched tumor specimens from African- and Caucasian-American Women diagnosed with breast cancer
Authors: Grunda Jessica M , Steg Adam D , He Qinghua , Steciuk Mark R , Byan-Parker Suzanne , Johnson Martin R , Grizzle William E 
Published: June 2012

AbstractBackgroundRecent studies suggest that the poorer breast cancer outcome observed in African-American women (AAW) may, in part, result from underlying molecular factors. The purpose of this study was to investigate gene expression differences between Caucasian-American women (CAW) and AAW that may contribute to this poorer prognosis.MethodsThe expression of 84 genes involved in breast carcinoma prognosis, response to therapy, estrogen signaling, and tumor aggressiveness was assessed in age- and stage-matched CAW and AAW paraffin-embedded breast cancer specimens. The Wilcoxon–Mann–Whitney Test was used to identify genes with a significant difference in expression between CAW and AAW. To determine if the differentially expressed genes could segregate between the CAW and AAW, we performed semi-supervised principal component analysis (SSPCA).ResultsTwenty genes were differentially expressed between AAW and CAW. SSPCA incorporating these 20 genes segregated AAW and CAW into two distinct groups. AAW were significantly (p < 0.05) more likely to display aberrations in G1/S cell-cycle regulatory genes, decreased expression of cell-adhesion genes, and low to no expression of ESR1, PGR, ERBB2 and estrogen pathway targets.ConclusionsThe gene expression differences identified between AAW and CAW may contribute to more aggressive disease, resistance to therapy, enhanced metastatic potential and poor clinical outcome. These findings support the hypothesis that breast cancer specimens collected from AAW display distinct gene expression differences compared to similar tissues obtained from CAW. Additional population-based studies are necessary to determine if these gene expression variations contribute to the highly aggressive and treatment-resistant breast cancer phenotype frequently observed in AAW.
Effects of HSP90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG) on NEU/HER2 overexpressing mammary tumours in MMTV-NEU-NT mice monitored by Magnetic Resonance Spectroscopy
Authors: Rodrigues Loreta M , Chung Yuen-Li , Al Saffar Nada M S , Sharp Swee Y , Jackson Laura E , Banerji Udai , Stubbs Marion , Leach Martin O , Griffiths John R , Workman Paul 
Published: June 2012

Abstract

Background
The importance of ERBB2/NEU/HER2 in the response of breast tumours to the heat shock protein 90 (HSP90) inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG; tanespimycin) has been demonstrated in the clinic. ERBB2 is an oncoprotein client that is highly dependent on HSP90. This and other oncogenic client proteins (e.g. B-RAF, C-RAF, ALK and CDK4) are depleted by 17-AAG in both animal tumours and patients. Here we investigate by Magnetic Resonance Spectroscopy (MRS) the metabolic response of 17-AAG in spontaneous, NEU/HER2 driven mammary tumours in transgenic MMTV-NEU-NT mice and in cells isolated and cultured from these tumours.

Methods
Mammary tumours were monitored by 31P MRS in vivo and in tumour extracts, comparing control and 17-AAG treated mice. A cell line derived from NEU/HER2 mammary tumours was also cultured and the effect of 17-AAG was measured by 31P MRS in cell extracts. Molecular biomarkers were assessed by immunoblotting in extracts from cells and tumours. For comparison of tumour volume, metabolite concentrations and Western blot band intensities, two-tailed unpaired t-tests were used.

Results
The NEU/HER2 mammary tumours were very sensitive to 17-AAG and responded in a dose-dependent manner to 3 daily doses of 20, 40 and 80mg/kg of 17-AAG, all of which caused significant regression. At the higher doses, 31P MRS of tumour extracts showed significant decreases in phosphocholine (PC) and phosphoethanolamine (PE) whereas no significant changes were seen at the 20mg/kg dose. Extracts of isolated cells cultured from the mammary carcinomas showed a significant decrease in viable cell number and total PME after 17-AAG treatment. Western blots confirmed the expected action of 17-AAG in inducing HSP72 and significantly depleting HSP90 client proteins, including NEU/HER2 both in tumours and in isolated cells.

Conclusions
The data demonstrate the high degree of sensitivity of this clinically relevant NEU/HER2-driven tumour model to HSP90 inhibition by 17-AAG, consistent with the clinical data, and suggest that the metabolic signature of choline phospholipids obtained by MRS could be useful both as a preclinical and clinical tool for investigating surrogate markers of response to treatment.
Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex
Authors: Portis Ezio , Scaglione Davide , Acquadro Alberto , Mauromicale Giovanni , Mauro Rosario , Knapp Steven J , Lanteri Sergio 
Published: June 2012

AbstractBackgroundThe Asteraceae speciesCynara cardunculus(2n = 2x = 34) includes the two fully cross-compatible domesticatedtaxaglobe artichoke (var.scolymusL.) and cultivated cardoon (var.altilisDC). As both are out-pollinators and suffer from marked inbreeding depression, linkage analysis has focussed on the use of a two way pseudo-test cross approach.ResultsA set of 172 microsatellite (SSR) loci derived from expressed sequence tag DNA sequence were integrated into the referenceC. cardunculusgenetic maps,based on segregation among the F1progeny of a cross between a globe artichoke and a cultivated cardoon. The resulting maps each detected 17 major linkage groups, corresponding to the species’ haploid chromosome number. A consensus map based on 66 co-dominant shared loci (64 SSRs and two SNPs) assembled 694 loci, with a mean inter-marker spacing of 2.5 cM. When the maps were used to elucidate the pattern of inheritance of head production earliness, a key commercial trait, seven regions were shown to harbour relevant quantitative trait loci (QTL). Together, these QTL accounted for up to 74% of the overall phenotypic variance.ConclusionThe newly developed consensus as well as the parental genetic maps can accelerate the process of tagging and eventually isolating the genes underlying earliness in both the domesticatedC. cardunculusforms. The largest single effect mapped to the same linkage group in each parental maps, and explained about one half of the phenotypic variance, thus representing a good candidate for marker assisted selection.
Evidence of mosquito-transmitted flavivirus circulation in Piedmont, north-western Italy
Authors: Cerutti Francesco , Giacobini Mario , Mosca Andrea , Grasso Ivan , Rambozzi Luisa , Rossi Luca , Bertolotti Luigi 
Published: June 2012

Abstract

Background

Flavivirus is a highly heterogeneous viral genus that includes important human pathogens and several viral strains with unknown zoonotic potential. Mosquito-borne flaviviruses have been isolated and characterized in Northern Italy: West Nile virus and Usutu virus were detected in mosquitoes and in different host species and recent studies provided evidence about the circulation of “insect Flavivirus” strains.

Methods
In order to clarify the diffusion and the distribution of the mosquito-transmitted flaviviruses in Italy, we analyzed Culex and Ochlerotatus mosquitoes collected in 2009 and 2010 in an area divided evenly between hills and plains and where the landscape is dominated by mixed agricultural patches, rice fields, deciduous tree forests, and urban environments. Each mosquito pool was tested for the presence of Flavivirus strains and we characterized positive samples by genetic sequencing.

Results
Positive mosquito pools revealed low infection prevalence, but suggested a continuous circulation of both Usutu virus and insect Flavivirus. Interestingly, phylogenetic analyses based on NS5 gene partial sequences showed a closer relationship among new Usutu virus strains from Piedmont and the reference sequences from the Eastern Europe, with respect to Italian samples characterized so far. Moreover, NS5 gene phylogeny suggested that mosquito flaviviruses found in Italy could belong to different lineages.

Conclusions
Our results contribute to a wider point of view on the heterogeneity of viruses infecting mosquitoes suggesting a taxonomical revision of the Mosquito-borne Flavivirus group.