bluuebunny/crossref_metadata_2025_split huggingface dataset:
Imaging techniques in lung cancer
Authors: De Wever W. , Coolen J. , Verschakelen J.A. 
Published: July 2011

SummaryConventional chest radiography, computed tomography (CT), magnetic resonance (MR) and positron emission tomography (PET) are all imaging techniques used for the detection, characterisation, staging and follow-up of lung cancer. The success of CT is related to the fact that very detailed imaging information of the localisation and the extent of the tumour, the presence of enlarged lymph nodes and the presence of metastatic disease can be provided. Integrated PET/CT combines anatomical information from CT with metabolic information from PET. PET/CT is nowadays the best imaging technique for the staging of lung cancer. MR was used for a long time as a problem-solving tool; however, with the development of new application methods, MR becomes a promising imaging modality in the evaluation of lung cancer patients. In this review, the use of these imaging techniques in the evaluation of lung cancer will be discussed.
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview
Authors: Skinner Jeff , Kotliarov Yuri , Varma Sudhir , Mine Karina L , Yambartsev Anatoly , Simon Richard , Huyen Yentram , Morgun Andrey 
Published: July 2011

Abstract

Background
DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes.

Results
Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools.

Conclusions
DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.
Detection of quantitative trait loci affecting serum cholesterol, LDL, HDL, and triglyceride in pigs
Authors: Uddin Muhammad Jasim , Duy Do Ngoc , Cinar Mehmet Ulas , Tesfaye Dawit , Tholen Ernst , Juengst Heinz , Looft Christian , Schellander Karl 
Published: July 2011

AbstractBackgroundSerum lipids are associated with many serious cardiovascular diseases and obesity problems. Many quantitative trait loci (QTL) have been reported in the pig mostly for performance traits but very few for the serum lipid traits. In contrast, remarkable numbers of QTL are mapped for serum lipids in humans and mice. Therefore, the objective of this research was to investigate the chromosomal regions influencing the serum level of the total cholesterol (CT), triglyceride (TG), high density protein cholesterol (HDL) and low density protein cholesterol (LDL) in pigs. For this purpose, a total of 330 animals from a Duroc × Pietrain F2 resource population were phenotyped for serum lipids using ELISA and were genotyped by using 122 microsatellite markers covering all porcine autosomes for QTL study in QTL Express. Blood sampling was performed at approximately 175 days before slaughter of the pig.ResultsMost of the traits were correlated with each other and were influenced by average daily gain, slaughter date and age. A total of 18 QTL including three QTL with imprinting effect were identified on 11 different porcine autosomes. Most of the QTL reached to 5% chromosome-wide (CW) level significance including a QTL at 5% experiment-wide (GW) and a QTL at 1% GW level significance. Of these QTL four were identified for both the CT and LDL and two QTL were identified for both the TG and LDL. Moreover, three chromosomal regions were detected for the HDL/LDL ratio in this study. One QTL for HDL on SSC2 and two QTL for TG on SSC11 and 17 were detected with imprinting effect. The highly significant QTL (1% GW) was detected for LDL at 82 cM on SSC1, whereas significant QTL (5% GW) was identified for HDL/LDL on SSC1 at 87 cM. Chromosomal regions with pleiotropic effects were detected for correlated traits on SSC1, 7 and 12. Most of the QTL identified for serum lipid traits correspond with the previously reported QTL for similar traits in other mammals. Two novel QTL on SSC16 for HDL and HDL/LDL ratio and an imprinted QTL on SSS17 for TG were detected in the pig for the first time.ConclusionThe newly identified QTL are potentially involved in lipid metabolism. The results of this work shed new light on the genetic background of serum lipid concentrations and these findings will be helpful to identify candidate genes in these QTL regions related to lipid metabolism and serum lipid concentrations in pigs.
Genetic polymorphisms of innate immunity-related inflammatory pathways and their association with factors related to type 2 diabetes
Authors: Arora Paul , Garcia-Bailo Bibiana , Dastani Zari , Brenner Darren , Villegas Andre , Malik Suneil , Spector Timothy D , Richards Brent , El-Sohemy Ahmed , Karmali Mohamed , Badawi Alaa 
Published: July 2011

AbstractBackgroundType 2 diabetes mellitus (T2DM) has been linked to a state of pre-clinical chronic inflammation resulting from abnormalities in the innate immune pathway. Serum levels of pro-inflammatory cytokines and acute-phase proteins, collectively known as 'inflammatory network', are elevated in the pre-, or early, stages of T2DM and increase with disease progression. Genetic variation can affect the innate immune response to certain environmental factors, and may, therefore, determine an individual's lifetime risk of disease.MethodsWe conducted a cross-sectional study in 6,720 subjects from the TwinsUK Registry to evaluate the association between 18 single nucleotide polymorphisms (SNPs) in five genes (TLR4,IL1A,IL6,TNFA, andCRP) along the innate immunity-related inflammatory pathway and biomarkers of predisposition to T2DM [fasting insulin and glucose, HDL- and LDL- cholesterols, triglycerides (TGs), amyloid-A, sensitive C-reactive protein (sCRP) and vitamin D binding protein (VDBP) and body mass index (BMI)].ResultsOf 18 the SNPs examined for their association with nine metabolic phenotypes of interest, six were significantly associated with five metabolic phenotypes (Bonferroni correction,P ≤ 0.0027). Fasting insulin was associated with SNPs inIL6andTNFA, serum HDL-C with variants ofTNFAandCRPand serum sCRP level with SNPs inCRP. Cross-correlation analysis among the different metabolic factors related to risk of T2DM showed several significant associations. For example, BMI was directly correlated with glucose (r = 0.11), insulin (r = 0.15), sCRP (r = 0.23), LDL-C (r = 0.067) and TGs (r = 0.18) but inversely with HDL-C (r = -0.14). sCRP was also positively correlated (P < 0.0001) with insulin (r = 0.17), amyloid-A (r = 0.39), TGs (r = 0.26), and VDBP (r = 0.36) but inversely with HDL-C (r = -0.12).ConclusionGenetic variants in the innate immunity pathway and its related inflammatory cascade is associated with some metabolic risk factors for T2DM; an observation that may provide a rationale for further studying their role as biomarkers for disease early risk prediction.
Radiotherapy may improve overall survival of patients with T3/T4 transitional cell carcinoma of the renal pelvis or ureter and delay bladder tumour relapse
Authors: Chen Bing , Zeng Zhao-Chong , Wang Guo-Min , Zhang Li , Lin Zong-Ming , Sun Li-An , Zhu Tong-Yu , Wu Li-Li , Zhang Jian-Ying , Ji Yuan 
Published: July 2011

Abstract

Background
Since transitional cell carcinoma (TCC) of the upper urinary tract is a relatively uncommon malignancy, the role of adjuvant radiotherapy is unknown.

Methods
We treated 133 patients with TCC of the renal pelvis or ureter at our institution between 1998 and 2008. The 67 patients who received external beam radiotherapy (EBRT) following surgery were assigned to the radiation group (RT). The clinical target volume included the renal fossa, the course of the ureter to the entire bladder, and the paracaval and para-aortic lymph nodes, which were at risk of harbouring metastatic disease in 53 patients. The tumour bed or residual tumour was targeted in 14 patients. The median radiation dose administered was 50 Gy. The 66 patients who received intravesical chemotherapy were assigned to the non-radiation group (non-RT).

Results
The overall survival rates for the RT and non-RT groups were not significantly different (p = 0.198). However, there was a significant difference between the survival rates for these groups based on patients with T3/T4 stage cancer. A significant difference was observed in the bladder tumour relapse rate between the irradiated and non-irradiated bladder groups (p = 0.004). Multivariate analysis indicated that improved overall survival was associated with age < 60 years, T1 or T2 stage, absence of synchronous LN metastases, and EBRT. Acute gastrointestinal and bladder reactions were the most common symptoms, but mild non-severe (> grade 3) hematologic symptoms also occurred.

Conclusion
EBRT may improve overall survival for patients with T3/T4 cancer of the renal pelvis or ureter and delay bladder tumour recurrence in all patients.
Bone turnover in passive smoking female rat: relationships to change in bone mineral density
Authors: Gao Shu-guang , Li Kang-hua , Xu Mai , Jiang Wei , Shen Hong , Luo Wei , Xu Wen-shuo , Tian Jian , Lei Guang-hua 
Published: July 2011

Abstract

Background
Many studies have identified smoking as a risk factor for osteoporosis, but it is unclear whether passive smoking has an effect on bone mineral density and bone turnover and if such an effect could cause osteoporosis.The purpose of the study was to investigate the effect of passive smoking on bone mineral density (BMD) and bone turnover and the relationship between BMD and bone turnover in female rat.

Methods
Forty-eight female Wistar rats were randomized into six groups: 2-month, 3-month,4-month smoke-exposed rats and their controls. A rat model of passive cigarette smoking was prepared by breeding female rats in a cigarette-smoking box for 2, 3 or 4 months. Serums were analyzed for levels of osteocalcin, bone-specific alkaline phosphatase (b-ALP) and Tartrate-resistant acid phosphatase 5b (TRACP 5b). BMD was assessed at lumbar vertebrae and femur by dual energy X-ray absorptiometry in passive smoking rats and in control rats.

Results
BMD of lumbar spine and femur was lower in 4-month smoke-exposed female rats than that in controls. However, there was no significant difference in serum osteocalcin levels between smoke-exposed rats and controls. Significantly lower b-ALP and higher TRACP 5b were found in the 3-month or 4-month smoke-exposed rats compared to controls. Subsequent analysis showed that b-ALP positively correlated with BMD of the lumbar vertebrae(r = 0.764, P = 0.027) and femur(r = 0.899, P = 0.002) in 4-month smoke-exposed female rats. Furthermore, TRACP 5b levels negatively correlated with BMD of lumbar vertebrae (r = -0.871, P = 0.005) and femur (r = -0.715, P = 0.046) in 4-month smoke-exposed female rats.

Conclusion
Our data suggest that smoke exposure can inhibit bone formation and increase bone resorption. The hazardous effects of passive smoking on bone status are associated with increased bone turnover in female rat.
Plasmodium vivax: comparison of immunogenicity among proteins expressed in the cell-free systems of Escherichia coli and wheat germ by suspension array assays
Authors: Rui Edmilson , Fernandez-Becerra Carmen , Takeo Satoru , Sanz Sergi , Lacerda Marcus VG , Tsuboi Takafumi , del Portillo Hernando A 
Published: July 2011

Abstract

Background
In vitro cell-free systems for protein expression with extracts from prokaryotic (Escherichia coli) or eukaryotic (wheat germ) cells coupled to solid matrices have offered a valid approach for antigen discovery in malaria research. However, no comparative analysis of both systems is presently available nor the usage of suspension array technologies, which offer nearly solution phase kinetics.

Methods
Five Plasmodium vivax antigens representing leading vaccine candidates were expressed in the E. coli and wheat germ cell-free systems at a 50 μl scale. Products were affinity purified in a single-step and coupled to luminex beads to measure antibody reactivity of human immune sera.

Results
Both systems readily produced detectable proteins; proteins produced in wheat germ, however, were mostly soluble and intact as opposed to proteins produced in E. coli, which remained mostly insoluble and highly degraded. Noticeably, wheat germ proteins were recognized in significantly higher numbers by sera of P. vivax patients than identical proteins produced in E. coli.

Conclusions
The wheat germ cell-free system offers the possibility of expressing soluble P. vivax proteins in a small-scale for antigen discovery and immuno-epidemiological studies using suspension array technology.
Chronologically scheduled snacking with high-protein products within the habitual diet in type-2 diabetes patients leads to a fat mass loss: a longitudinal study
Authors: Navas-Carretero Santiago , Abete Itziar , Zulet M Angeles , Martínez J Alfredo 
Published: July 2011

Abstract

Background
Obesity is the most relevant overnutrition disease worldwide and is associated to different metabolic disorders such as insulin resistance and type-2 diabetes. Low glycemic load foods and diets and moderately high protein intake have been shown to reduce body weight and fat mass, exerting also beneficial effects on LDL-cholesterol, triglyceride concentrations, postprandial glucose curve and HDL-cholesterol levels. The present study aimed at studying the potential functionality of a series of low glycemic index products with moderately high protein content, as possible coadjuvants in the control of type-2 diabetes and weight management following a chronologically planned snacking offer (morning and afternoon).

Methods
The current trial followed a single group, sequential, longitudinal design, with two consecutive periods of 4 weeks each. A total of 17 volunteers participated in the study. The first period was a free living period, with volunteers' habitual ad libitum dietary pattern, while the second period was a free-living period with structured meal replacements at breakfast, morning snack and afternoon snack, which were exchanged by specific products with moderately high protein content and controlled low glycemic index, following a scheduled temporal consumption. Blood extractions were performed at the beginning and at the end of each period (free-living and intervention). Parameters analysed were: fasting glucose, insulin, glycosylated hemoglobin, total-, HDL- and LDL-cholesterol, triglyceride, C - reactive protein and Homocysteine concentrations. Postprandial glucose and insulin were also measured. Anthropometrical parameters were monitored each 2 weeks during the whole study.

Results
A modest but significant (p = 0.002) reduction on body weight (1 kg) was observed during the intervention period, mainly due to the fat mass loss (0.8 kg, p = 0.02). This weight reduction was observed without apparently associated changes in total energy intake. None of the biochemical biomarkers measured was altered throughout the whole study.

Conclusions
Small changes in the habitual dietary recommendations in type-2 diabetes patients by the inclusion of specific low-glycemic, moderately high-protein products in breakfast, morning and afternoon snacks may promote body weight and fat-mass loss, without apparently altering biochemical parameters and cardiovascular risk-related factors.

Trial Registration
Trial registered at clinicaltrials.gov NCT01264523.
Integrin subunits alpha5 and alpha6 regulate cell cycle by modulating the chk1 and Rb/E2F pathways to affect breast cancer metastasis
Authors: Wang Yanfang , Shenouda Sylvia , Baranwal Somesh , Rathinam Rajamani , Jain Prachi , Bao Lili , Hazari Siddhartha , Dash Srikanta , Alahari Suresh K 
Published: July 2011

AbstractBackgroundAlthough integrins have been implicated in the progression of breast cancer, the exact mechanism whereby they exert this regulation is clearly not understood. To understand the role of integrins in breast cancer, we examined the expression levels of several integrins in mouse breast cancer cell lines by flow cytometry and the data were validated by Western and RT-PCR analysis. The importance of integrins in cell migration and cell invasion was examined byin vitroassays. Further the effect of integrins on metastasis was investigated byin vivoexperimental metastasis assays using mouse models.ResultsIntegrin α5 subunit is highly expressed in the nonmetastatic cell line 67NR and is significantly low in the highly invasive cell line 4T1. In contrast, expression levels of integrin α6 subunit are high in 4T1 cells and low in 67NR cells.In vitrodata indicated that overexpression of α5 subunit and knockdown of α6 integrin subunit inhibited cell proliferation, migration, and invasion. Ourin vivofindings indicated that overexpression of integrin α5 subunit and knockdown of α6 subunit decreased the pulmonary metastasis property of 4T1 cells. Our data also indicated that overexpression of alpha 5 integrin subunit and suppression of alpha6 integrin subunit inhibited cells entering into S phase by up-regulating p27, which results in downregulation of cyclinE/CDK2 complexes, This suggests that these integrins regulate cell growth through their effects on cell-cycle-regulated proteins. We also found that modulation of these integrins upregulates E2F, which may induce the expression of chk1 to regulate cdc25A/cyclin E/CDK2/Rb in a feedback loop mechanism.ConclusionThis study indicates that Integrin α5 subunit functions as a potential metastasis suppressor, while α6 subunit functions as a metastasis promoter. The modulation of integrins reduces cdc25 A, another possible mechanism for downregulation of CDK2. Taken together we demonstrate a link between integrins and the chk1-cdc25-cyclin E/CDK2-Rb pathway.
The role of 18F-FDG-PET/CT in the preoperative staging and posttherapy follow up of gastriccancer:Comparison with spiral CT
Authors: Ozkan Elgin , Araz Mine , Soydal Cigdem , Kucuk Ozlem N. 
Published: July 2011

Abstract

Background
The aim of this study was to investigate the role of F-18 fluoro-deoxy-glucose (FDG) positron emission tomography and computed tomography (PET/CT) in the preoperative and posttherapy restaging of gastric cancer and to compare with spiral computerized tomography (CT).

Method
A total of 42 PET/CT scans of 36 gastric cancer patients (28M, 8F; mean age: 56,0 ± 15) were included in the study. A retrospective analysis of the PET/CT results of the patients were compared with concurrent CT results. Confirmation was made by clinical course and serial imaging studies in the follow up. The compatibility ratios were calculated and the accuracy of the PET/CT was assessed. Agreement between PET/CT and concurrent CT was calculated using kappa statistics.

Results
Patients were separated into 3 groups: the patients who were referred to our clinic for preoperative staging (4 patients), for posttherapy evaluation (24 patients) and for the suspicion of local recurrence and/or metastasis exploration after a disease free period (8 patients). Groups 1 and 3 included a small number of patients so they were omitted from the statistical analysis. Focusing on Goup 2, the overall concordance rate was 50% (12 patients). Region based analysis showed the rates of concordance for local recurrence, local lymph node metastasis and distant metastasis were 91% (Kappa: 0.70), 95% (Kappa:0.86) and 50% (Kappa:0.26) respectively. Distant metastases were also investigated in detail and the two techniques showed a concordance of 91% (Kappa: 0.75) for liver, 79%(Kappa:0.31) for distant lymph node, 79% (0.42) for lung, 87%(Kappa:0.33) for bone and 95% for intestinal wall metastasis.

Conclusion
PET/CT is a complementary imaging method which can be successfully used in both preoperative and posttherapy evaluation of gastric cancer.
A novel MCF-10A line allowing conditional oncogene expression in 3D culture
Authors: Herr Ricarda , Wöhrle Franziska U , Danke Christina , Berens Christian , Brummer Tilman 
Published: July 2011

Abstract

Introduction
Non-transformed mammary epithelial cell lines such as MCF-10A recapitulate epithelial morphogenesis in three-dimensional (3D) tissue culture by forming acinar structures. They represent an important tool to characterize the biological properties of oncogenes and to model early carcinogenic events. So far, however, these approaches were restricted to cells with constitutive oncogene expression prior to the set-up of 3D cultures. Although very informative, this experimental setting has precluded the analysis of effects caused by sudden oncoprotein expression or withdrawal in established epithelial cultures. Here, we report the establishment and use of a stable MCF-10A cell line (MCF-10Atet) fitted with a novel and improved doxycycline (dox)-regulated expression system allowing the conditional expression of any transgene.

Methods
MCF-10Atet cells were generated by stable transfection with pWHE644, a vector expressing a second generation tetracycline-regulated transactivator and a novel transcriptional silencer. In order to test the properties of this new repressor/activator switch, MCF-10Atet cells were transfected with a second plasmid, pTET-HABRAF-IRES-GFP, which responds to dox treatment with the production of a bi-cistronic transcript encoding hemagglutinin-tagged B-Raf and green fluorescent protein (GFP). This improved conditional expression system was then characterized in detail in terms of its response to various dox concentrations and exposure times. The plasticity of the phenotype provoked by oncogenic B-RafV600E in MCF-10Atet cells was analyzed in 3D cultures by dox exposure and subsequent wash-out.

Results
MCF-10Atet cells represent a tightly controlled, conditional gene expression system. Using B-RafV600E as a model oncoprotein, we show that its sudden expression in established 3D cultures results in the loss of acinar organization, the induction of an invasive phenotype and hallmarks of epithelial-to-mesenchymal transition (EMT). Importantly, we show for the first time that this severe transformed phenotype can be reversed by dox wash-out and concomitant termination of oncogene expression.

Conclusions
Taken together, we have generated a stable MCF-10A subline allowing tight dox-controlled and reversible expression of any transgene without the need to modify its product by introducing artificial dimerization or ligand-binding domains. This system will be very valuable to address phenomena such as EMT, oncogene addiction, oncogene-induced senescence and drug resistance.
Topological confinement in an antisymmetric potential in bilayer graphene in the presence of a magnetic field
Authors: Zarenia Mohammad , Pereira Joao Milton , Peeters François Maria , de Aquino Farias Gil 
Published: July 2011

Abstract
We investigate the effect of an external magnetic field on the carrier states that are localized at a potential kink and a kink-antikink in bilayer graphene. These chiral states are localized at the interface between two potential regions with opposite signs.
PACS numbers: 71.10.Pm, 73.21.-b, 81.05.Uw
The investigation of frequency response for the magnetic nanoparticulate assembly induced by time-varied magnetic field
Authors: Sun Jianfei , Sui Yunxia , Wang Chunyu , Gu Ning 
Published: July 2011

AbstractThe field-induced assembly of γ-Fe2O3nanoparticles under alternating magnetic field of different frequency was investigated. It was found that the assembly was dependent upon the difference between colloidal relaxation time and field period. The same experiments on DMSA-coated γ-Fe2O3nanoparticles exhibited that the relaxation time may be mainly determined by the magnetic size rather than the physical size. Our results may be valuable for the knowledge of dynamic assembly of colloidal particles.