bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR
Authors: Maroufi Asad , Van Bockstaele Erik , De Loose Marc 
Published: March 2010

Abstract

Background
Quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) is a sensitive technique for quantifying gene expression levels. One or more appropriate reference genes must be selected to accurately compare mRNA transcripts across different samples and tissues. Thus far, only actin-2 has been used as a reference gene for qRT-PCR in chicory, and a full comparison of several candidate reference genes in chicory has not yet been reported.

Results
Seven candidate reference genes, including nicotinamide adenine dinucleotide dehydrogenase (NADHD), actin (ACT), β-tubulin (TUB), glyceraldehyde-3-phosphate-dehydrogenase (GADPH), histone H3 (H3), elongation factor 1-alpha (EF) and 18S rRNA (rRNA) were selected to study the expression stability for normalisation of gene expression in chicory. Primer specificity and amplification efficiency were verified for each gene. The expression stability of these genes was analysed across chicory root and leaf tissues using geNorm, NormFinder and BestKeeper software. ACT, EF, and rRNA were the most stable genes as identified by the three different analysis methods. In addition, the use of ACT, EF and GAPDH as reference genes was illustrated by analysing 1-FEHII (FEHII) expression in chicory root and leaf tissues. These analyses revealed the biological variation in FEHII transcript expression among the tissues studied, and between individual plants.

Conclusions
geNorm, NormFinder, and BestKeeper analyses indicated that ACT, EF and rRNA had the highest expression stability across leaf and root tissues, while GAPDH and NADHD showed relatively low expression stability. The results of this study emphasise the importance of validating reference genes for qRT-PCR analysis in chicory. The use of the most stable reference genes such as ACT and EF allows accurate normalisation of gene expression in chicory leaf and root tissues.
Genome-wide gene copy number and expression analysis of primary gastric tumors and gastric cancer cell lines
Authors: Junnila Siina , Kokkola Arto , Karjalainen-Lindsberg Marja-Liisa , Puolakkainen Pauli , Monni Outi 
Published: March 2010

Abstract

Background
Gastric cancer is one of the most common malignancies worldwide and the second most common cause of cancer related death. Gene copy number alterations play an important role in the development of gastric cancer and a change in gene copy number is one of the main mechanisms for a cancer cell to control the expression of potential oncogenes and tumor suppressor genes.

Methods
To highlight genes of potential biological and clinical relevance in gastric cancer, we carried out a systematic array-based survey of gene expression and copy number levels in primary gastric tumors and gastric cancer cell lines and validated the results using an affinity capture based transcript analysis (TRAC assay) and real-time qRT-PCR.

Results
Integrated microarray analysis revealed altogether 256 genes that were located in recurrent regions of gains or losses and had at least a 2-fold copy number- associated change in their gene expression. The expression levels of 13 of these genes, ALPK2, ASAP1, CEACAM5, CYP3A4, ENAH, ERBB2, HHIPL2, LTB4R, MMP9, PERLD1, PNMT, PTPRA, and OSMR, were validated in a total of 118 gastric samples using either the qRT-PCR or TRAC assay. All of these 13 genes were differentially expressed between cancerous samples and nonmalignant tissues (p < 0.05) and the association between copy number and gene expression changes was validated for nine (69.2%) of these genes (p < 0.05).

Conclusion
In conclusion, integrated gene expression and copy number microarray analysis highlighted genes that may be critically important for gastric carcinogenesis. TRAC and qRT-PCR analyses validated the microarray results and therefore the role of these genes as potential biomarkers for gastric cancer.
Hepatotoxicity and effectiveness of a Nevirapine-based antiretroviral therapy in HIV-infected patients with or without viral hepatitis B or C infection in Cameroon
Authors: Mbougua Jules B Tchatchueng , Laurent Christian , Kouanfack Charles , Bourgeois Anke , Ciaffi Laura , Calmy Alexandra , Gwet Henri , Koulla-Shiro Sinata , Ducos Jacques , Mpoudi-Ngolé Eitel , Molinari Nicolas , Delaporte Eric 
Published: March 2010

AbstractBackgroundCoinfection with hepatitis B virus (HBV) or hepatitis C virus (HCV) in HIV-infected patients receiving a commonly used nevirapine-based antiretroviral therapy is a major concern for African clinicians owing to its high prevalence, the infrequent testing and treatment of viral hepatitis, and the impact of liver disease on the tolerability and effectiveness of anti-HIV treatment. We compared the hepatotoxicity and the immunological, virological and clinical effectiveness of a nevirapine-based antiretroviral therapy between patients infected with HIV only and patients coinfected with hepatitis B or C virus in Cameroon.MethodsA retrospective cohort study was conducted among HIV-1-infected patients. Plasma HBV DNA and HCV RNA were tested in positive or indeterminate samples for HBsAg or HCV antibodies, respectively. All patients received nevirapine and lamivudine plus stavudine or zidovudine.ResultsOf 169 HIV-1-infected patients with a median baseline CD4 count of 135 cells/mm3(interquartile range [IQR] 67-218), 21% were coinfected with HBV or HCV. In coinfected patients, the median viral load was 2.47 × 107IU/mL for HBV (IQR 3680-1.59 × 108) and 928 000 IU/mL for HCV (IQR 178 400-2.06 × 106). Multivariate analyses showed that the risk of hepatotoxicity was 2-fold higher in coinfected patients (p< 0.01). The response to antiretroviral therapy was however comparable between monoinfected and coinfected patients in terms of CD4 cell count increase (p= 0.8), HIV-1 viral load below 400 copies/mL (p= 0.9), death (p= 0.3) and death or new AIDS-defining event (p= 0.1). Nevirapine was replaced by a protease inhibitor in 4 patients owing to hepatotoxicity.ConclusionThis study suggests that the nevirapine-based antiretroviral therapy could be used safely as first-line treatment in patients with low CD4 cell count in Africa despite frequent coinfections with HBV or HCV and infrequent testing of these infections. Although testing for HBV and HCV should be systematically performed before initiating antiretroviral therapy, transaminases elevations at baseline or during treatment should be a decisive argument for testing when hepatitis status is unknown.
Anti-tumor therapy with macroencapsulated endostatin producer cells
Authors: Rodrigues Danielle B , Chammas Roger , Malavasi Natália V , da Costa Patrícia LN , Chura-Chambi Rosa M , Balduino Keli N , Morganti Ligia 
Published: March 2010

Abstract

Background
Theracyte is a polytetrafluoroethylene membrane macroencapsulation system designed to induce neovascularization at the tissue interface, protecting the cells from host's immune rejection, thereby circumventing the problem of limited half-life and variation in circulating levels. Endostatin is a potent inhibitor of angiogenesis and tumor growth. Continuous delivery of endostatin improves the efficacy and potency of the antitumoral therapy. The purpose of this study was to determine whether recombinant fibroblasts expressing endostatin encapsulated in Theracyte immunoisolation devices can be used for delivery of this therapeutic protein for treatment of mice bearing B16F10 melanoma and Ehrlich tumors.

Results
Mice were inoculated subcutaneously with melanoma (B16F10 cells) or Ehrlich tumor cells at the foot pads. Treatment began when tumor thickness had reached 0.5 mm, by subcutaneous implantation of 107 recombinant encapsulated or non-encapsulated endostatin producer cells. Similar melanoma growth inhibition was obtained for mice treated with encapsulated or non-encapsulated endostatin-expressing cells. The treatment of mice bearing melanoma tumor with encapsulated endostatin-expressing cells was decreased by 50.0%, whereas a decrease of 56.7% in tumor thickness was obtained for mice treated with non-encapsulated cells. Treatment of Ehrlich tumor-bearing mice with non-encapsulated endostatin-expressing cells reduced tumor thickness by 52.4%, whereas lower tumor growth inhibition was obtained for mice treated with encapsulated endostatin-expressing cells: 24.2%. Encapsulated endostatin-secreting fibroblasts failed to survive until the end of the treatment. However, endostatin release from the devices to the surrounding tissues was confirmed by immunostaining. Decrease in vascular structures, functional vessels and extension of the vascular area were observed in melanoma microenvironments.

Conclusions
This study indicates that immunoisolation devices containing endostatin-expressing cells are effective for the inhibition of the growth of melanoma and Ehrlich tumors.
Macroencapsulation of engineered cells is therefore a reliable platform for the refinement of innovative therapeutic strategies against tumors.
Acute variceal bleeding in a patient with idiopathic myelofibrosis successfully treated with endoscopic variceal band ligation and chemotherapy: a case report
Authors: Tamaki Kumiko , Otaka Michiro , Sakamoto Naoto , Matsumoto Kenshi , Yamashina Shunhei , Watanabe Sumio 
Published: March 2010

Abstract

Introduction
Idiopathic myelofibrosis is a chronic myeloproliferative disorder characterized by leukoerythroblastosis, massive splenomegaly, and increases in the reticular and collagen fibers in the bone marrow. Portal hypertension is observed in some patients with idiopathic myelofibrosis. Gastrointestinal hemorrhages, which are due mostly to the rupture of the esophageal varices, have been sporadically reported to be an infrequent complication of idiopathic myelofibrosis.

Case presentation
We report a case of a Japanese 63-year-old woman with myelofibrosis and variceal hemorrhage, with a background of concomitant portal and pulmonary hypertension. She was successfully treated through a combination of endoscopic variceal ligation and chemotherapy.

Conclusion
This is the first known report on the successful application of endoscopic variceal ligation and chemotherapy as the therapeutic procedure for an esophageal variceal hemorrhage in a patient with myelofibrosis.
Detecting variable (V), diversity (D) and joining (J) gene segment recombination using a two-colour fluorescence system
Authors: Scott Gina B , de Wynter Erika A , Cook Graham P 
Published: March 2010

Abstract

Background
Diversity of immunoglobulins and the T cell antigen receptors is achieved via the recombination activating gene (RAG)-mediated rearrangement of variable (V), diversity (D) and joining (J) gene segments, and this underpins the efficient recognition of a seemingly limitless array of antigens. Analysis of V(D)J recombination activity is typically performed using extrachromosomal recombination substrates that are recovered from transfected cells and selected using bacterial transformation. We have developed a two-colour fluorescence-based system that simplifies detection of both deletion and inversion joining events mediated by RAG proteins.

Results
This system employs two fluorescent reporter genes that differentially mark unrearranged substrates and those that have undergone RAG-mediated deletion or inversion events. The recombination products bear the hallmarks of true V(D)J recombination and activity can be detected using fluorescence microscopy or flow cytometry. Recombination events can be detected without the need for cytotoxic selection of recombination products and the system allows analysis of recombination activity using substrates integrated into the genome.

Conclusions
This system will be useful in the analysis and exploitation of the V(D)J recombination machinery and suggests that similar approaches could be used to replace expression of one gene with another during lymphocyte development.
The anti-cyclic citrullinated peptide response in tuberculosis patients is not citrulline-dependent and sensitive to treatment
Authors: Elkayam Ori , Segal Refael , Bendayan Daniele , van Uitert Robert , Onnekink Carla , Pruijn Ger JM 
Published: March 2010

Abstract
Introduction
Patients with tuberculosis (TB) frequently produce anti-citrullinated protein antibodies (ACPA). The objective of this study is to characterize the citrulline-dependence of the ACPA reactivity in sera of patients with mycobacterium infections.

Methods
Serum samples of 134 patients with untreated mycobacterium infections (122 TB, 12 nontuberculous mycobacterium) were tested for antibodies against both the citrullinated (Cit) and the non-citrullinated (Arg) form of 2 cyclic synthetic peptides. In 33 patients, a follow-up sample was tested six months after starting anti-mycobacterial drugs.

Results
A substantial proportion of patients with mycobacterial infections demonstrated antibodies against 0401Cit, 0401Arg, 0722Cit and 0722Arg. Fourteen patients demonstrated anti-0401Cit, 83 anti-0401Arg, 22 anti-0722Cit and 61 anti-0722Arg, while none of these antibodies were detected in the 20 healthy controls. All the patients but one, who were anti-0401Cit and anti-0722Cit positive, demonstrated reactivity against the respective Arg peptide. In the subset of 33 patients with a follow-up test six months after starting treatment, the mean levels of antibodies to 0401Cit, 0401Arg, 0722Cit and 0722Arg significantly decreased after treatment. All the patients who were anti-0401Cit and anti-0722Cit positive turned negative after treatment. The presence of anti-0401Cit/Arg and anti-0722Cit/Arg was found to be significantly correlated with the presence of HIV.

Conclusions
ACPA may be found in patients with TB. In most of the cases, the reactivity is citrulline independent. A positive cyclic citrullinated peptide (CCP) test in these patients should therefore be interpreted with care, and preferably followed by a control ELISA with a non-citrullinated antigen.
Anabolic and catabolic responses of human articular chondrocytes to varying oxygen percentages
Authors: Ströbel Simon , Loparic Marko , Wendt David , Schenk Andreas D , Candrian Christian , Lindberg Raija LP , Moldovan Florina , Barbero Andrea , Martin Ivan 
Published: March 2010

Abstract
Introduction
Oxygen is a critical parameter proposed to modulate the functions of chondrocytes ex-vivo as well as in damaged joints. This article investigates the effect of low (more physiological) oxygen percentage on the biosynthetic and catabolic activity of human articular chondrocytes (HAC) at different phases of in vitro culture.

Methods
HAC expanded in monolayer were cultured in pellets for two weeks (Phase I) or up to an additional two weeks (Phase II). In each Phase, cells were exposed to 19% or 5% oxygen. Resulting tissues and culture media were assessed to determine amounts of produced/released proteoglycans and collagens, metalloproteinases (MMPs), collagen degradation products and collagen fibril organization using biochemical, (immuno)-histochemical, gene expression and scanning electron microscopy analyses. In specific experiments, the hypoxia-inducible factor-1α (HIF-1α) inhibitor cadmium chloride was supplemented in the culture medium to assess the involvement of this pathway.

Results
Independent from the oxygen percentage during expansion, HAC cultured at 5% O2 (vs 19% O2) during Phase I accumulated higher amounts of glycosaminoglycans and type II collagen and expressed reduced levels of MMP-1 and MMP-13 mRNA and protein. Switching to 19% oxygen during Phase II resulted in reduced synthesis of proteoglycan and collagen, increased release of MMPs, accumulation of type II collagen fragments and higher branching of collagen fibrils. In contrast, reducing O2 during Phase II resulted in increased proteoglycan and type II collagen synthesis and reduced expression and release of MMP-13 mRNA and protein. Supplementation of cadmium chloride during differentiation culture at 5% O2 drastically reduced the up-regulation of type II collagen and the down-regulation of MMP-1 mRNA.

Conclusions
The application of more physiologic oxygen percentage during specific phases of differentiation culture enhanced the biosynthetic activity and reduced the activity of catabolic enzymes implicated in cartilage breakdown. Modulation of the oxygen percentage during HAC culture may be used to study pathophysiological events occurring in osteoarthritis and to enhance properties of in vitro engineered cartilaginous tissues.
Prolonged mechanical ventilation in a respiratory-care setting: a comparison of outcome between tracheostomized and translaryngeal intubated patients
Authors: Wu Yao-Kuang , Tsai Ying-Huang , Lan Chou-Chin , Huang Chun-Yao , Lee Chih-Hsin , Kao Kuo-Chin , Fu Jui-Ying 
Published: March 2010

Abstract
Introduction
Mechanical ventilation of patients may be accomplished by either translaryngeal intubation or tracheostomy. Although numerous intensive care unit (ICU) studies have compared various outcomes between the two techniques, no definitive consensus indicates that tracheostomy is superior. Comparable studies have not been performed in a respiratory care center (RCC) setting.

Methods
This was a retrospective observational study of 985 tracheostomy and 227 translaryngeal intubated patients who received treatment in a 24-bed RCC between November 1999 and December 2005. Treatment and mortality outcomes were compared between tracheostomized and translaryngeal intubated patients, and the factors associated with positive outcomes in all patients were determined.

Results
Duration of RCC (22 vs. 14 days) and total hospital stay (82 vs. 64 days) and total mechanical ventilation days (53 vs. 41 days) were significantly longer in tracheostomized patients (all P < 0.05). The rate of in-hospital mortality was significantly higher in the translaryngeal group (45% vs. 31%;P < 0.05). No significant differences were found in weaning success between the groups (both were >55%) or in RCC mortality. Because of significant baseline between-group heterogeneity, case-match analysis was performed. This analysis confirmed the whole cohort findings, except for the fact that a trend for in-hospital mortality was noted to be higher in the translaryngeal group (P = 0.08). Stepwise logistic regression revealed that patients with a lower median severity of disease (APACHE II score <18) who were properly nourished (albumin >2.5 g/dl) or had normal metabolism (BUN <40 mg/dl) were more likely to be successfully weaned and survive (all P < 0.05). Patients who were tracheostomized were also significantly more likely to survive (P < 0.05)

Conclusions
These findings suggest that the type of mechanical ventilation does not appear to be an important determinant of weaning success in an RCC setting. Focused care administered by experienced providers may be more important for facilitating weaning success than the ventilation method used. However, our findings do suggest that tracheostomy may increase the likelihood of patient survival.
Collaboratively charting the gene-to-phenotype network of human congenital heart defects
Authors: Barriot Roland , Breckpot Jeroen , Thienpont Bernard , Brohée Sylvain , Van Vooren Steven , Coessens Bert , Tranchevent Leon-Charles , Van Loo Peter , Gewillig Marc , Devriendt Koenraad , Moreau Yves 
Published: March 2010

Abstract
Background
How to efficiently integrate the daily practice of molecular biologists, geneticists, and clinicians with the emerging computational strategies from systems biology is still much of an open question.

Description
We built on the recent advances in Wiki-based technologies to develop a collaborative knowledge base and gene prioritization portal aimed at mapping genes and genomic regions, and untangling their relations with corresponding human phenotypes, congenital heart defects (CHDs). This portal is not only an evolving community repository of current knowledge on the genetic basis of CHDs, but also a collaborative environment for the study of candidate genes potentially implicated in CHDs - in particular by integrating recent strategies for the statistical prioritization of candidate genes. It thus serves and connects the broad community that is facing CHDs, ranging from the pediatric cardiologist and clinical geneticist to the basic investigator of cardiogenesis.

Conclusions
This study describes the first specialized portal to collaboratively annotate and analyze gene-phenotype networks. Of broad interest to the biological community, we argue that such portals will play a significant role in systems biology studies of numerous complex biological processes.
CHDWiki is accessible at http://www.esat.kuleuven.be/~bioiuser/chdwiki
Psychological Distress in Adult Survivors of Childhood Cancer: The Swiss Childhood Cancer Survivor Study
Authors: Michel Gisela , Rebholz Cornelia E. , von der Weid Nicolas X. , Bergstraesser Eva , Kuehni Claudia E. 
Published: March 2010

Purpose To evaluate the degree of psychological distress in adult childhood cancer survivors in Switzerland and to characterize survivors with significant distress. Methods Childhood cancer survivors who were age younger than 16 years when diagnosed between 1976 and 2003, had survived more than 5 years, and were currently age 20 years or older received a postal questionnaire. Psychological distress was assessed using the Brief Symptom Inventory (BSI). Raw scores were transformed into T scores according to the German norm sample, and the proportion of participants being at increased risk for psychological distress was calculated (case rule: T ≥ 63). t tests and univariable and multivariable logistic regressions were used for statistical analyses. Results One thousand seventy-six survivors (63.% of eligible survivors, 71.9% of contacted survivors) returned the questionnaire, 987 with complete data on BSI. Comparison with the norm populations showed lower T scores (T < 50) in the Global Severity Index (GSI; T = 46.2), somatization (T = 47.6), obsessive-compulsive tendencies (T = 46.9), and anxiety (T = 48.4). However, more childhood cancer survivors (especially women) had increased distress for GSI (14.4%), interpersonal sensitivity (16.5%), depression (13.4%), aggression (16.9%), and psychotic tendencies (15.6%) than the expected 10% from the norm population. Caseness was associated with female sex, being a single child, older age at study, and self-reported late effects, especially psychological problems. Conclusion Results show that childhood cancer survivors, on average, have less psychological distress than a norm population but that the proportion of survivors at risk for high psychological distress is disproportionally large. Monitoring psychological distress in childhood cancer survivors may be desirable during routine follow-up, and psychological support should be offered as needed.