bluuebunny/crossref_metadata_2025_split huggingface dataset:
Everolimus Augments the Effects of Sorafenib in a Syngeneic Orthotopic Model of Hepatocellular Carcinoma
Authors: Piguet Anne-Christine , Saar Bettina , Hlushchuk Ruslan , St-Pierre Marie V. , McSheehy Paul M.J. , Radojevic Vesna , Afthinos Maresa , Terracciano Luigi , Djonov Valentin , Dufour Jean-François 
Published: April 2011

Abstract
Sorafenib targets the Raf/mitogen-activated protein kinase, VEGF, and platelet-derived growth factor pathways and prolongs survival patients in advanced hepatocellular carcinoma (HCC). Everolimus inhibits the mammalian target of rapamycin, a kinase overactive in HCC. To investigate whether the antitumor effects of these agents are additive, we compared a combined and sequential treatment regimen of everolimus and sorafenib with monotherapy. After hepatic implantation of Morris Hepatoma (MH) cells, rats were randomly allocated to everolimus (5 mg/kg, 2×/week), sorafenib (7.5 mg/kg/d), combined everolimus and sorafenib, sequential sorafenib (2 weeks) then everolimus (3 weeks), or control groups. MRI quantified tumor volumes. Erk1/2, 4E-BP1, and their phosphorylated forms were quantified by immunoblotting. Angiogenesis was assessed in vitro by aortic ring and tube formation assays, and in vivo with Vegf-a mRNA and vascular casts. After 35 days, tumor volumes were reduced by 60%, 85%, and 55%, relative to controls, in everolimus, the combination, and sequential groups, respectively (P &lt; 0.01). Survival was longest in the combination group (P &lt; 0.001). Phosphorylation of 4E-BP1 and Erk1/2 decreased after everolimus and sorafenib, respectively. Angiogenesis decreased after all treatments (P &lt; 0.05), although sorafenib increased Vegf-a mRNA in liver tumors. Vessel sprouting was abundant in control tumors, lower after sorafenib, and absent after the combination. Intussusceptive angiogenic transluminal pillars failed to coalesce after the combination. Combined treatment with everolimus and sorafenib exerts a stronger antitumoral effect on MH tumors than monotherapy. Everolimus retains antitumoral properties when administered sequentially after sorafenib. This supports the clinical use of everolimus in HCC, both in combination with sorafenib or after sorafenib. Mol Cancer Ther; 10(6); 1007–17. ©2011 AACR.
Trastuzumab Regulates IGFBP-2 and IGFBP-3 to Mediate Growth Inhibition: Implications for the Development of Predictive Biomarkers for Trastuzumab Resistance
Authors: Dokmanovic Milos , Shen Yi , Bonacci Tabetha M. , Hirsch Dianne S. , Wu Wen Jin 
Published: April 2011

AbstractActivation of insulin-like growth factor-I receptor (IGF-IR) signaling is an important mechanism for trastuzumab resistance. IGF-binding proteins (IGFBP) modulate IGF-IR signaling and play important roles in the control of breast cancer progression. In this article, we report that trastuzumab treatment enhances the expression and secretion of IGFBP-3 in SKBR3 cells, a trastuzumab-sensitive breast cancer cell line, and that this upregulation of IGFBP-3 induced by trastuzumab correlates with trastuzumab-mediated growth inhibition. We describe a new role for IGFBP-3 in the regulation of IGF-I–mediated cross-talk between IGF-IR and ErbB2 signaling pathways. In particular, treatment of SKBR3 cells with recombinant IGFBP-3 blocks IGF-I–induced activation of IGF-IR and ErbB2, and stable expression of IGFBP-3 inhibits SKBR3 cell growth. We find an inverse relationship in the levels of secreted IGFBP-3 such that high levels of IGFBP-3 are associated with trastuzumab-sensitive breast cancer cells (SKBR3 and BT-474), whereas low levels of IGFBP-3 are found in trastuzumab-resistant cells (clone 3 and JIMT-1). In contrast to IGFBP-3, the secretion and expression of IGFBP-2 are upregulated in trastuzumab-resistant SKBR3 cells. Furthermore, we show that IGFBP-2 stimulates activation of ErbB2 and that trastuzumab reduces IGFBP-2–stimulated ErbB2 activation. Based on our data, we propose a novel mechanism of action whereby trastuzumab enhances the expression and secretion of IGFBP-3, which interferes with IGF-I–mediated mitogenic signaling via autocrine and paracrine mechanisms and reduces IGFBP-2–induced ErbB2 activation to mediate growth inhibition. Changes in secretion profiles of IGFBP-2 and IGFBP-3 in trastuzumab-sensitive and trastuzumab-resistant cells may promote the development of IGFBP-2 and IGFBP-3 as predictive biomarkers for trastuzumab resistance. Mol Cancer Ther; 10(6); 917–28. ©2011 AACR.
Physical Activity and the Risk of Incident Atrial Fibrillation in Women
Authors: Everett Brendan M. , Conen David , Buring Julie E. , Moorthy M.V. , Lee I-Min , Albert Christine M. 
Published: April 2011

Background—
Physical activity (PA) is well known to reduce the risk of cardiovascular disease. We hypothesized that regular PA, possibly acting through reductions in blood pressure and body mass index (BMI), would reduce the risk of incident atrial fibrillation (AF) in women.

Methods and Results—

We prospectively followed 34 759 women who reported their leisure-time PA levels for the occurrence of AF. We estimated energy expenditure in metabolic equivalent (MET)-h/wk and validated self-reported AF with medical records. The mean (SD) age of the 34 759 participants was 54.6 (7.0) years, the mean BMI was 26.0 (5.0) kg/m
2
, 26.5% had hypertension, and the median (IQR) PA was 8.4 (2.8, 20.4) MET-h/wk. After a median of 14.4 years of observation, 968 women had development of AF. In age-, cholesterol-, smoking-, alcohol-, diabetes-, and race-adjusted models, increasing quintiles of PA were associated with reduced risks of AF (hazard ratio for extreme quintiles, 0.82; 0.66 to 1.01;
P
trend=0.007 over quintiles). Although this association was not substantially different after adjusting for hypertension (0.87; 0.70 to 1.07;
P
trend 0.02), it was attenuated after adjustment for BMI (0.99; 0.80 to 1.23;
P
trend=0.22). Women who achieved the federal government's recommendation of 7.5 MET-h/wk of PA were at reduced risk of AF compared with those who did not (0.86; 0.75 to 0.98;
P
=0.03). This association was also attenuated by BMI (0.96; 0.84 to 1.10;
P
=0.57).

Conclusions—
In middle-aged women, physical activity was associated with a modestly reduced risk of AF. However, this relationship was no longer significant after controlling for body mass index.
A Theory of Deep Stratification and Overturning Circulation in the Ocean
Authors: Nikurashin Maxim , Vallis Geoffrey 
Published: April 2011

AbstractA simple theoretical model of the deep stratification and meridional overturning circulation in an idealized single-basin ocean with a circumpolar channel is presented. The theory includes the effects of wind, eddies, and diapycnal mixing; predicts the deep stratification in terms of the surface forcing and other problem parameters; makes no assumption of zero residual circulation; and consistently accounts for the interaction between the circumpolar channel and the rest of the ocean.The theory shows that dynamics of the overturning circulation can be characterized by two limiting regimes, corresponding to weak and strong diapycnal mixing. The transition between the two regimes is described by a nondimensional number characterizing the strength of the diffusion-driven compared to the wind-driven overturning circulation. In the limit of weak diapycnal mixing, deep stratification throughout the ocean is produced by the effects of wind and eddies in a circumpolar channel and maintained even in the limit of vanishing diapycnal diffusivity and in a flat-bottomed ocean. The overturning circulation across the deep stratification is driven by the diapycnal mixing in the basin away from the channel but is sensitive, through changes in stratification, to the wind and eddies in the channel. In the limit of strong diapycnal mixing, deep stratification is primarily set by eddies in the channel and diapycnal mixing in the basin away from the channel, with the wind over the circumpolar channel playing a secondary role. Analytical solutions for the deep stratification and overturning circulation in the limit of weak diapycnal mixing and numerical solutions that span the regimes of weak to strong diapycnal mixing are presented.The theory is tested with a coarse-resolution ocean general circulation model configured in an idealized geometry. A series of experiments performed to examine the sensitivity of the deep stratification and the overturning circulation to variations in wind stress and diapycnal mixing compare well with predictions from the theory.
Norovirus gastroenteritis causes severe and lethal complications after chemotherapy and hematopoietic stem cell transplantation
Authors: Schwartz Stefan , Vergoulidou Maria , Schreier Eckart , Loddenkemper Christoph , Reinwald Mark , Schmidt-Hieber Martin , Flegel Willy A. , Thiel Eckhard , Schneider Thomas 
Published: April 2011

Abstract
Norovirus (NV) infections are a frequent cause of gastroenteritis (GE), but data on this disease in immunocompromised patients are limited. We analyzed an NV outbreak, which affected immunosuppressed patients in the context of chemotherapy or HSCT. On recognition, 7 days after admission of the index patient, preventive measures were implemented. Attack rates were only 3% (11/334) and 10% (11/105) among patients and staff members, respectively. The median duration of symptoms was 7 days in patients compared with only 3 days in staff members (P = .02). Three patients died of the NV infection. Commonly used clinical diagnostic criteria (Kaplan-criteria) were unsuitable because they applied to 11 patients with proven NV-GE but also to 15 patients without NV-GE. With respect to the therapeutic management, it is important to differentiate intestinal GVHD from NV-GE. Therefore, we analyzed the histopathologic patterns in duodenal biopsies, which were distinctive in both conditions. Stool specimens in patients remained positive for NV-RNA for a median of 30 days, but no transmission was observed beyond an asymptomatic interval of 48 hours. NV-GE is a major threat to patients with chemotherapy or HSCT, and meticulous measures are warranted to prevent transmission of NV to these patients.
Pro-inflammatory endothelial cell dysfunction is associated with intersectin-1s down-regulation
Authors: Singla Sunit , Predescu Dan , Bardita Cristina , Wang Minhua , Zhang Jian , Balk Robert A , Predescu Sanda 
Published: April 2011

Abstract

Background
The response of lung microvascular endothelial cells (ECs) to lipopolysaccharide (LPS) is central to the pathogenesis of lung injury. It is dual in nature, with one facet that is pro-inflammatory and another that is cyto-protective. In previous work, overexpression of the anti-apoptotic Bcl-XL rescued ECs from apoptosis triggered by siRNA knockdown of intersectin-1s (ITSN-1s), a pro-survival protein crucial for ECs function. Here we further characterized the cyto-protective EC response to LPS and pro-inflammatory dysfunction.

Methods and Results
Electron microscopy (EM) analyses of LPS-exposed ECs revealed an activated/dysfunctional phenotype, while a biotin assay for caveolae internalization followed by biochemical quantification indicated that LPS causes a 40% inhibition in biotin uptake compared to controls. Quantitative PCR and Western blotting were used to evaluate the mRNA and protein expression, respectively, for several regulatory proteins of intrinsic apoptosis, including ITSN-1s. The decrease in ITSN-1s mRNA and protein expression were countered by Bcl-XL and survivin upregulation, as well as Bim downregulation, events thought to protect ECs from impending apoptosis. Absence of apoptosis was confirmed by TUNEL and lack of cytochrome c (cyt c) efflux from mitochondria. Moreover, LPS exposure caused induction and activation of inducible nitric oxide synthase (iNOS) and a mitochondrial variant (mtNOS), as well as augmented mitochondrial NO production as measured by an oxidation oxyhemoglobin (oxyHb) assay applied on mitochondrial-enriched fractions prepared from LPS-exposed ECs. Interestingly, expression of myc-ITSN-1s rescued caveolae endocytosis and reversed induction of iNOS expression.

Conclusion
Our results suggest that ITSN-1s deficiency is relevant for the pro-inflammatory ECs dysfunction induced by LPS.
Community analysis of bacteria colonizing intestinal tissue of neonates with necrotizing enterocolitis
Authors: Smith Birgitte , Bodé Susan , Petersen Bodil L , Jensen Tim K , Pipper Christian , Kloppenborg Julie , Boyé Mette , Krogfelt Karen A , Mølbak Lars 
Published: April 2011

AbstractBackgroundNecrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in newborn neonates. Bacteria are believed to be important in the pathogenesis of NEC but bacterial characterization has only been done on human faecal samples and experimental animal studies. The aim of this study was to investigate the microbial composition and the relative number of bacteria in inflamed intestinal tissue surgically removed from neonates diagnosed with NEC (n = 24). The bacterial populations in the specimens were characterized by laser capture microdissection and subsequent sequencing combined with fluorescent in situ hybridization (FISH), using bacterial rRNA-targeting oligonucleotide probes.ResultsBacteria were detected in 22 of the 24 specimens, 71% had moderate to high densities of bacteria. The phyla detected by 16S rRNA gene sequencing were:Proteobacteria(49.0%),Firmicutes(30.4%),Actinobacteria(17.1%) andBacteroidetes(3.6%). A major detected class of the phylumProteobacteriabelonged toδ-proteobacteria. Surprisingly,Clostridiumspecies were only detected in 4 of the specimens by FISH, but two of these specimens exhibited histological pneumatosis intestinalis and both specimens had a moderate to a high density ofC. butyricumandC. parputrificumdetected by using species specific FISH probes. A 16S rRNA gene sequence tag similar toRalstoniaspecies was detected in most of the neonatal tissues and members of this genus have been reported to be opportunistic pathogens but their role in NEC has still to be clarified.ConclusionIn this study, in situ identification and community analysis of bacteria found in tissue specimens from neonates with NEC, were analysed for the first time. Although a large variability of bacteria was found in most of the analyzed specimens, no single or combination of known potential pathogenic bacteria species was dominating the samples suggestive NEC as non-infectious syndrome. However there was a significant correlation between the presence ofC. butyricum&C. parputrificumand histological pneumatosis intestinalis. Finally this study emphasizes the possibility to examine the microbial composition directly on excised human tissues to avoid biases from faecal samples or culturing.
A cDNA microarray, UniShrimpChip, for identification of genes relevant to testicular development in the black tiger shrimp (Penaeus monodon)
Authors: Leelatanawit Rungnapa , Uawisetwathana Umaporn , Klinbunga Sirawut , Karoonuthaisiri Nitsara 
Published: April 2011

Abstract
Background
Poor reproductive maturation in captive male broodstock of the black tiger shrimp (Penaeus monodon) is one of the serious problems to the farming industries. Without genome sequence, EST libraries of P. monodon were previously constructed to identify transcripts with important biological functions. In this study, a new version of cDNA microarray, UniShrimpChip, was constructed from the Peneaus monodon EST libraries of 12 tissues, containing 5,568 non-redundant cDNA clones from 10,536 unique cDNA in the P. monodon EST database. UniShrimpChip was used to study testicular development by comparing gene expression levels of wild brooders from the West and East coasts of Thailand and domesticated brooders with different ages (10-, 14-, 18-month-old).

Results
The overall gene expression patterns from the microarray experiments revealed distinct transcriptomic patterns between the wild and domesticated groups. Moreover, differentially expressed genes from the microarray comparisons were identified, and the expression patterns of eight selected transcripts were subsequently confirmed by reverse-transcriptase quantitative PCR (RT-qPCR). Among these, expression levels of six subunits (CSN2, 4, 5, 6, 7a, and 8) of the COP9 signalosome (CSN) gene family in wild and different ages of domesticated brooders were examined by RT-qPCR. Among the six subunits, CSN5 and CSN6 were most highly expressed in wild brooders and least expressed in the 18-month-old domesticated group; therefore, their full-length cDNA sequences were characterized.

Conclusions
This study is the first report to employ cDNA microarray to study testicular development in the black tiger shrimp. We show that there are obvious differences between the wild and domesticated shrimp at the transcriptomic level. Furthermore, our study is the first to investigate the feasibility that the CSN gene family might have involved in reproduction and development of this economically important species.
Inflammatory mediators in breast cancer: Coordinated expression of TNFα & IL-1β with CCL2 & CCL5 and effects on epithelial-to-mesenchymal transition
Authors: Soria Gali , Ofri-Shahak Maya , Haas Ilana , Yaal-Hahoshen Neora , Leider-Trejo Leonor , Leibovich-Rivkin Tal , Weitzenfeld Polina , Meshel Tsipi , Shabtai Esther , Gutman Mordechai , Ben-Baruch Adit 
Published: April 2011

Abstract

Background
The inflammatory chemokines CCL2 (MCP-1) & CCL5 (RANTES) and the inflammatory cytokines TNFα & IL-1β were shown to contribute to breast cancer development and metastasis. In this study, we wished to determine whether there are associations between these factors along stages of breast cancer progression, and to identify the possible implications of these factors to disease course.

Methods
The expression of CCL2, CCL5, TNFα and IL-1β was determined by immunohistochemistry in patients diagnosed with: (1) Benign breast disorders (=healthy individuals); (2) Ductal Carcinoma In Situ (DCIS); (3) Invasive Ducal Carcinoma without relapse (IDC-no-relapse); (4) IDC-with-relapse. Based on the results obtained, breast tumor cells were stimulated by the inflammatory cytokines, and epithelial-to-mesenchymal transition (EMT) was determined by flow cytometry, confocal analyses and adhesion, migration and invasion experiments.

Results
CCL2, CCL5, TNFα and IL-1β were expressed at very low incidence in normal breast epithelial cells, but their incidence was significantly elevated in tumor cells of the three groups of cancer patients. Significant associations were found between CCL2 & CCL5 and TNFα & IL-1β in the tumor cells in DCIS and IDC-no-relapse patients. In the IDC-with-relapse group, the expression of CCL2 & CCL5 was accompanied by further elevated incidence of TNFα & IL-1β expression. These results suggest progression-related roles for TNFα and IL-1β in breast cancer, as indeed indicated by the following: (1) Tumors of the IDC-with-relapse group had significantly higher persistence of TNFα and IL-1β compared to tumors of DCIS or IDC-no-relapse; (2) Continuous stimulation of the tumor cells by TNFα (and to some extent IL-1β) has led to EMT in the tumor cells; (3) Combined analyses with relevant clinical parameters suggested that IL-1β acts jointly with other pro-malignancy factors to promote disease relapse.

Conclusions
Our findings suggest that the coordinated expression of CCL2 & CCL5 and TNFα & IL-1β may be important for disease course, and that TNFα & IL-1β may promote disease relapse. Further in vitro and in vivo studies are needed for determination of the joint powers of the four factors in breast cancer, as well as analyses of their combined targeting in breast cancer.
An adaptable method using human mixed tissue ratiometric controls for benchmarking performance on gene expression microarrays in clinical laboratories
Authors: Pine P Scott , Rosenzweig Barry A , Thompson Karol L 
Published: April 2011

Abstract

Background
Molecular biomarkers that are based on mRNA transcripts are being developed for the diagnosis and treatment of a number of diseases. DNA microarrays are one of the primary technologies being used to develop classifiers from gene expression data for clinically relevant outcomes. Microarray assays are highly multiplexed measures of comparative gene expression but have a limited dynamic range of measurement and show compression in fold change detection. To increase the clinical utility of microarrays, assay controls are needed that benchmark performance using metrics that are relevant to the analysis of genomic data generated with biological samples.

Results
Ratiometric controls were prepared from commercial sources of high quality RNA from human tissues with distinctly different expression profiles and mixed in defined ratios. The samples were processed using six different target labeling protocols and replicate datasets were generated on high density gene expression microarrays. The area under the curve from receiver operating characteristic plots was calculated to measure diagnostic performance. The reliable region of the dynamic range was derived from log2 ratio deviation plots made for each dataset. Small but statistically significant differences in diagnostic performance were observed between standardized assays available from the array manufacturer and alternative methods for target generation. Assay performance using the reliable range of comparative measurement as a metric was improved by adjusting sample hybridization conditions for one commercial kit.

Conclusions
Process improvement in microarray assay performance was demonstrated using samples prepared from commercially available materials and two metrics - diagnostic performance and the reliable range of measurement. These methods have advantages over approaches that use a limited set of external controls or correlations to reference sets, because they provide benchmark values that can be used by clinical laboratories to help optimize protocol conditions and laboratory proficiency with microarray assays.
Target-selective homologous recombination cloning for high-throughput generation of monoclonal antibodies from single plasma cells
Authors: Kurosawa Nobuyuki , Yoshioka Megumi , Isobe Masaharu 
Published: April 2011

AbstractBackgroundMolecular cloning of functional immunoglobulin genes from single plasma cells is one of the most promising technologies for the rapid development of monoclonal antibody drugs. However, the proper insertion of PCR-amplified immunoglobulin genes into expression vectors remains an obstacle to the high-throughput production of recombinant monoclonal antibodies.ResultsWe developed a single-step cloning method, target-selective homologous recombination (TS-HR), in which PCR-amplified immunoglobulin variable genes were selectively inserted into vectors, even in the presence of nonspecifically amplified DNA. TS-HR utilizes Red/ET-mediated homologous recombination with a target-selective vector (TS-vector) with unique homology arms on its termini. Using TS-HR, immunoglobulin variable genes were cloned directly into expression vectors by co-transforming unpurified PCR products and the TS-vector intoE. coli. Furthermore, the high cloning specificity of TS-HR allowed plasmids to be extracted from pools of transformed bacteria without screening single colonies for correct clones. We present a one-week protocol for the production of recombinant mouse monoclonal antibodies from large numbers of single plasma cells.ConclusionThe time requirements and limitations of traditional cloning procedures for the production of recombinant immunoglobulins have been significantly reduced with the development of the TS-HR cloning technique.