bluuebunny/crossref_metadata_2025_split huggingface dataset:
CADM1 is a strong neuroblastoma candidate gene that maps within a 3.72 Mb critical region of loss on 11q23
Authors: Michels Evi , Hoebeeck Jasmien , De Preter Katleen , Schramm Alexander , Brichard Bénédicte , De Paepe Anne , Eggert Angelika , Laureys Geneviève , Vandesompele Jo , Speleman Frank 
Published: July 2008

Abstract

Background
Recurrent loss of part of the long arm of chromosome 11 is a well established hallmark of a subtype of aggressive neuroblastomas. Despite intensive mapping efforts to localize the culprit 11q tumour suppressor gene, this search has been unsuccessful thus far as no sufficiently small critical region could be delineated for selection of candidate genes.

Methods
To refine the critical region of 11q loss, the chromosome 11 status of 100 primary neuroblastoma tumours and 29 cell lines was analyzed using a BAC array containing a chromosome 11 tiling path. For the genes mapping within our refined region of loss, meta-analysis on published neuroblastoma mRNA gene expression datasets was performed for candidate gene selection. The DNA methylation status of the resulting candidate gene was determined using re-expression experiments by treatment of neuroblastoma cells with the demethylating agent 5-aza-2'-deoxycytidine and bisulphite sequencing.

Results
Two small critical regions of loss within 11q23 at chromosomal band 11q23.1-q23.2 (1.79 Mb) and 11q23.2-q23.3 (3.72 Mb) were identified. In a first step towards further selection of candidate neuroblastoma tumour suppressor genes, we performed a meta-analysis on published expression profiles of 692 neuroblastoma tumours. Integration of the resulting candidate gene list with expression data of neuroblastoma progenitor cells pinpointed CADM1 as a compelling candidate gene. Meta-analysis indicated that CADM1 expression has prognostic significance and differential expression for the gene was noted in unfavourable neuroblastoma versus normal neuroblasts. Methylation analysis provided no evidence for a two-hit mechanism in 11q deleted cell lines.

Conclusion
Our study puts CADM1 forward as a strong candidate neuroblastoma suppressor gene. Further functional studies are warranted to elucidate the role of CADM1 in neuroblastoma development and to investigate the possibility of CADM1 haploinsufficiency in neuroblastoma.
Suppression of local invasion of ameloblastoma by inhibition of matrix metalloproteinase-2 in vitro
Authors: Wang Anxun , Zhang Bin , Huang Hongzhang , Zhang Leitao , Zeng Donglin , Tao Qian , Wang Jianguang , Pan Chaobin 
Published: July 2008

Abstract

Background
Ameloblastomas are odontogenic neoplasms characterized by local invasiveness. This study was conducted to address the role of matrix metalloproteinase-2 (MMP-2) in the invasiveness of ameloblastomas.

Methods
Plasmids containing either MMP-2 siRNA or tissue inhibitor of metalloproteinase-2 (TIMP-2) cDNA were created and subsequently transfected into primary ameloblastoma cells. Zymography, RT-PCR, and Western blots were used to assess MMP-2 activity and expression of MMP-2 and TIMP-2, as well as protein levels.

Results
Primary cultures of ameloblastoma cells expressed cytokeratin (CK) 14 and 16, and MMP-2, but only weakly expressed CK18 and vimentin. MMP-2 mRNA and protein levels were significantly inhibited by RNA interference (P < 0.05). Both MMP-2 siRNA and TIMP-2 overexpression inhibited MMP-2 activity and the in vitro invasiveness of ameloblastoma.

Conclusion
These results indicate that inhibition of MMP-2 activity suppresses the local invasiveness of ameloblastoma cells. This mechanism may serve as a novel therapeutic target in ameloblastomas pursuant to additional research.
Association of loss of epithelial syndecan-1 with stage and local metastasis of colorectal adenocarcinomas: An immunohistochemical study of clinically annotated tumors
Authors: Hashimoto Yosuke , Skacel Marek , Adams Josephine C 
Published: July 2008

Abstract

Background
Syndecan-1 is a transmembrane proteoglycan with important roles in cell-cell and cell-extracellular matrix adhesion and as a growth factor co-receptor. Syndecan-1 is highly expressed by normal epithelial cells and loss of expression has been associated with epithelial-mesenchymal transition and the transformed phenotype. Loss of epithelial syndecan-1 has been reported in human colorectal adenocarcinomas, but whether this has prognostic significance remains undecided. Here we have examined syndecan-1 expression and its potential prognostic value with reference to a clinically annotated tissue microarray for human colon adenocarcinomas.

Methods
Syndecan-1 expression was examined by immunohistochemistry of a tissue microarray containing cores from 158 colorectal adenocarcinomas and 15 adenomas linked to a Cleveland Clinic, IRB-approved database with a mean clinical follow-up of 38 months. The Kaplan-Meier method was used to analyze the relationship between syndecan-1 expression and patient survival. Potential correlations between syndecan-1 expression and the candidate prognostic biomarker fascin were examined.

Results
Syndecan-1 is expressed at the basolateral borders of normal colonic epithelial cells. On adenocarcinoma cells, syndecan-1 was present around cell membranes and in cytoplasm. In 87% of adenocarcinomas, syndecan-1 was decreased or absent; only 13% of patients had stained for syndecan-1 on more than 75% of tumor cells. Decreased syndecan-1 correlated with a higher TNM stage and lymph node metastasis and was more common in males (p = 0.042), but was not associated with age, tumor location or Ki67 index. Reduced tumor syndecan-1 staining also correlated with upregulation of stromal fascin (p = 0.016). Stromal syndecan-1 was observed in 16.6% of tumors. There was no difference in survival between patients with low or high levels of either tumor or stromal syndecan-1.

Conclusion
Syndecan-1 immunoreactivity was decreased in the majority of human colon adenocarcinomas in correlation with TNM stage and metastasis to local lymph nodes. In a small fraction of adenocarcinomas, syndecan-1 was upregulated in the local stroma. Syndecan-1 expression status did not correlate with patient survival outcomes. Combined analysis of syndecan-1 in relation to a potential prognostic biomarker, fascin, identified that loss of tumor syndecan-1 correlated significantly with strong stromal fascin staining.
Metastatic susceptibility locus, an 8p hot-spot for tumour progression disrupted in colorectal liver metastases: 13 candidate genes examined at the DNA, mRNA and protein level
Authors: Macartney-Coxson Donia P , Hood Kylie A , Shi Hong-jun , Ward Teresa , Wiles Anna , O'Connor Rosemary , Hall David A , Lea Rod A , Royds Janice A , Stubbs Richard S , Rooker Serena 
Published: July 2008

Abstract

Background
Mortality from colorectal cancer is mainly due to metastatic liver disease. Improved understanding of the molecular events underlying metastasis is crucial for the development of new methods for early detection and treatment of colorectal cancer. Loss of chromosome 8p is frequently seen in colorectal cancer and implicated in later stage disease and metastasis, although a single metastasis suppressor gene has yet to be identified. We therefore examined 8p for genes involved in colorectal cancer progression.

Methods
Loss of heterozygosity analyses were used to map genetic loss in colorectal liver metastases. Candidate genes in the region of loss were investigated in clinical samples from 44 patients, including 6 with matched colon normal, colon tumour and liver metastasis. We investigated gene disruption at the level of DNA, mRNA and protein using a combination of mutation, semi-quantitative real-time PCR, western blotting and immunohistochemical analyses.

Results
We mapped a 2 Mb region of 8p21-22 with loss of heterozygosity in 73% of samples; 8/11 liver metastasis samples had loss which was not present in the corresponding matched primary colon tumour. 13 candidate genes were identified for further analysis. Both up and down-regulation of 8p21-22 gene expression was associated with metastasis. ADAMDEC1 mRNA and protein expression decreased during both tumourigenesis and tumour progression. Increased STC1 and LOXL2 mRNA expression occurred during tumourigenesis. Liver metastases with low DcR1/TNFRSF10C mRNA expression were more likely to present with extrahepatic metastases (p = 0.005). A novel germline truncating mutation of DR5/TNFRSF10B was identified, and DR4/TNFRSF10A SNP rs4872077 was associated with the development of liver metastases (p = 0.02).

Conclusion
Our data confirm that genes on 8p21-22 are dysregulated during colorectal cancer progression. Interestingly, however, instead of harbouring a single candidate colorectal metastasis suppressor 8p21-22 appears to be a hot-spot for tumour progression, encoding at least 13 genes with a putative role in carcinoma development. Thus, we propose that this region of 8p comprises a metastatic susceptibility locus involved in tumour progression whose disruption increases metastatic potential.
Impact of case management by advanced practice nurses in primary care on unplanned hospital admissions: a controlled intervention study
Authors: Huws Dyfed W , Cashmore Deborah , Newcombe Robert G , Roberts Catherine , Vincent Judith , Elwyn Glyn 
Published: July 2008

Abstract

Background
Increasing unplanned hospital admissions disrupt planned health care, lead to additional morbidity and are expensive. A recent review found only weak evidence for case management preventing unplanned admissions, yet case management of older people is being implemented widely in the UK. We aimed to study the effect of advanced practice nurse case management on unplanned medical and geriatric hospital admission rates in patients 50 years and over, and on admission risk in a 'higher risk' sub-group of patients in the UK.

Methods
Case management by advanced practice nurses in NHS primary care practices in the Swansea Local Health Board area, Wales, UK. We conducted a prospective non-randomized controlled intervention study comparing unplanned medical and geriatric patient admissions between five intervention and thirty non-intervention practices during a pre-intervention year and an intervention year.

Results
For all lengths of stay, comparing intervention (n = 5) with non-intervention practices (n = 30) from pre-intervention to intervention year, we found that the unplanned medical and geriatric admission rate was significantly lower in the intervention group – adjusted relative risk of 0.909; relative risk reduction 9.1% (95% credible limit 0.840 to 0.984, p = 0.018); absolute risk reduction 0.99 admissions per 100 patients (95% credible limit 0.17 to 1.86, p = 0.018). For lengths of stay of one night or more we observed a stronger effect – adjusted relative risk 0.896; relative risk reduction 10.41% (95%, credible limit 0.820 to 0.979, p = 0.015). Most of the rate reduction was due to a reduction in the number of new admissions but much less so for admissions of lengths of stay of at least one night, compared to all lengths of stay. We did not find a statistically significant effect on re-admission or multiple re-admission rates in 'higher risk' patients previously admitted one or more times – adjusted relative risk of further multiple admissions per previously admitted patient 0.908 (95% credible limit 0.765, 1.077); relative risk reduction 9.3%; adjusted relative risk of total admissions per multiple admitter 0.995 (95% credible limit 0.940, 1.053) relative risk reduction 0.6%.

Conclusion
Although this study reports a reduction in unplanned admission rates in the intervention practices, this appears to be only in part directly due to nurse case management: most of the reduction did not occur in multipe admitters whom were case managed. Further research is needed to explain this finding, to elucidate how best to target the attention of case managers and to examine the complexity of potential outcomes in terms of the nature and necessity of admissions and most suitable lengths-of-stay in terms of acute care or rehabilittion need.
Equity in the use of antithrombotic drugs, beta-blockers and statins among Finnish coronary patients
Authors: Manderbacka Kristiina , Keskimäki Ilmo , Reunanen Antti , Klaukka Timo 
Published: July 2008

Abstract

Background
Earlier studies have mainly reported the use of antithrombotic drugs, beta-blockers and statins among hospital patient populations or MI patients. This study aimed to describe the use of these drugs among middle-aged Finnish coronary patients and to identify patient groups in risk of being prescribed inadequate medication for secondary prevention of coronary heart disease.

Methods
One-year follow-up survey data from a random sample of a cohort of coronary patients were used along with register data linked to the survey. The response rate was 54% (n = 2650). The main outcome measures were use of antithrombotic drugs, beta-blockers and statins and the data were analysed using logistic regression analysis.

Results
Among men and women, respectively, 82% and 81% used beta-blockers, 95% and 89% used antithrombotic drugs, and 62% and 59% used statins. Younger men and men from higher socioeconomic groups were more likely to use statins, even after controlling for disease severity and comorbidity. In women, the age trend was reversed and no socioeconomic differences were found. Drug use increased with increased disease severity, but diabetes had only a slight effect.

Conclusion
The use of antithrombotic drugs and beta-blockers among Finnish coronary patients seemed to be rather appropriate and, to some extent, prescription practices of preventive medication varied according to patients' risk of coronary events. However, statin use was remarkably low among men with low socio-economic status, and there is need to improve preventive drug treatment among diabetic coronary patients.
A family of GFP-like proteins with different spectral properties in lancelet Branchiostoma floridae
Authors: Baumann Diana , Cook Malcolm , Ma Limei , Mushegian Arcady , Sanders Erik , Schwartz Joel , Yu C Ron 
Published: July 2008

Abstract

Background
Members of the green fluorescent protein (GFP) family share sequence similarity and the 11-stranded β-barrel fold. Fluorescence or bright coloration, observed in many members of this family, is enabled by the intrinsic properties of the polypeptide chain itself, without the requirement for cofactors. Amino acid sequence of fluorescent proteins can be altered by genetic engineering to produce variants with different spectral properties, suitable for direct visualization of molecular and cellular processes. Naturally occurring GFP-like proteins include fluorescent proteins from cnidarians of the Hydrozoa and Anthozoa classes, and from copepods of the Pontellidae family, as well as non-fluorescent proteins from Anthozoa. Recently, an mRNA encoding a fluorescent GFP-like protein AmphiGFP, related to GFP from Pontellidae, has been isolated from the lancelet Branchiostoma floridae, a cephalochordate (Deheyn et al., Biol Bull, 2007 213:95).

Results
We report that the nearly-completely sequenced genome of Branchiostoma floridae encodes at least 12 GFP-like proteins. The evidence for expression of six of these genes can be found in the EST databases. Phylogenetic analysis suggests that a gene encoding a GFP-like protein was present in the common ancestor of Cnidaria and Bilateria. We synthesized and expressed two of the lancelet GFP-like proteins in mammalian cells and in bacteria. One protein, which we called LanFP1, exhibits bright green fluorescence in both systems. The other protein, LanFP2, is identical to AmphiGFP in amino acid sequence and is moderately fluorescent. Live imaging of the adult animals revealed bright green fluorescence at the anterior end and in the basal region of the oral cirri, as well as weaker green signals throughout the body of the animal. In addition, red fluorescence was observed in oral cirri, extending to the tips.

Conclusion
GFP-like proteins may have been present in the primitive Metazoa. Their evolutionary history includes losses in several metazoan lineages and expansion in cephalochordates that resulted in the largest repertoire of GFP-like proteins known thus far in a single organism. Lancelet expresses several of its GFP-like proteins, which appear to have distinct spectral properties and perhaps diverse functions.

Reviewers
This article was reviewed by Shamil Sunyaev, Mikhail Matz (nominated by I. King Jordan) and L. Aravind.
Effects of antidepressant treatment on heart rate variability in major depression: A quantitative review
Authors: van Zyl Louis T , Hasegawa Takuya , Nagata Katsutaro 
Published: July 2008

Abstract

Background
The literature measuring effects of antidepressant and electroconvulsive therapy (ECT) for major depression on heart rate variability (HRV) in medically well individuals was reviewed.

Methods
Fourteen studies evaluating HRV were included. Twenty three pre-post or within group comparisons were available. Treatment impact on measures of HRV was pooled over studies. We examined different classes of antidepressants, and for short and long electrocardiogram (ECG) recordings separately.

Results
Tricyclic antidepressants (TCAs) were associated with declines in most measures of HRV and significant increase in heart rate (HR) in studies with short recording intervals. No significant changes were found for longer recording times.
Treatment effects with selective serotonin reuptake inhibitors (SSRIs) were more variable. Short-recording studies revealed a significant decrease in HR and an increase in one HRV measure. In two 24-hour recording studies no significant changes were observed. No relationship between ECT and HRV has been established in the literature. The effects of other drugs are reported.

Limitations
Few studies measure the effects of treatment of depression on HRV. Existing studies have generally used very small samples, employing a variety of measurements and methodologies.

Conclusion
We confirm that TCAs are associated with a large decrease in HRV and increase HR. However, data for SSRIs is not clear. Although the effect of SSRIs on HRV is weaker than for TCAs, evidence shows that SSRIs are associated with a small decrease in HR, and an increase in one measure of HRV. The use of TCAs in depression leads to changes in HRV that are associated with increased risk of mortality.
Jejunal perforation caused by a feeding jejunostomy tube: a case report
Authors: Stylianides Nicholas A , Date Ravindra S , Pursnani Kishor G , Ward Jeremy B 
Published: July 2008

Abstract

Introduction
Percutaneous endoscopic gastrostomy and feeding jejunostomy are used for providing long-term nutritional support to patients with neurological disorders. Various mechanical complications of these procedures are described.

Case presentation
We report a case of a 17-year-old boy with cerebral injury who had a percutaneous endoscopic gastrostomy tube changed to a feeding jejunostomy tube. Twenty-four hours later he developed abdominal pain and became clinically septic. A contrast study through the feeding tube and a subsequent computed tomography scan did not reveal any intra-abdominal pathology. At laparotomy it was discovered that the tip of the feeding tube had perforated through the jejunal wall and was lying outside the lumen. This was successfully treated by re-inserting a feeding jejunostomy tube distally and closure of the perforation and previous FJ site

Conclusion
We suggest that the threshold for contrast studies and operative intervention should be low in neurologically impaired patients to avoid the delay in treatment of tube-related complications.
DM, but not cathepsin L, is required to control an aerosol infection withMycobacterium tuberculosis
Authors: Nepal Rajeev Mani , Vesosky Bridget , Turner Joanne , Bryant Paula 
Published: July 2008

AbstractAntigen presentation by class II MHC molecules in the uninfected host is a multi-step process involving key functions provided by specific cathepsins (Cat) and the peptide editor DM. Herein, we examined the requirement for each of these components in mice to control a low-dose aerosol infection with Mycobacterium tuberculosis (MTB). Mice lacking Cat B, -L, or -S were similar to wild-type in their ability to control the growth and dissemination of MTB. In contrast, DM−/− mice failed to limit MTB growth and showed ∼100-fold higher bacterial burden in the lung and spleen (5–6 weeks postinfection) as compared with wild-type and Cat-deficient mice. Histopathology revealed impaired cellular recruitment and altered granuloma formation in the lungs of MTB-infected DM−/− mice. Moreover, despite impaired thymic selection in Cat L−/− and DM−/− mice, MTB-specific CD4+ T cells were elicited only in the former. The lower numbers of MTB-specific CD4+ T cells available in Cat L−/− mice as compared with wild-type animals were sufficient to control MTB growth and dissemination. In addition, DM−/− macrophages infected with MTB in vitro were unable to stimulate pathogen-specific T cells. The data indicate that the majority of antigens derived from MTB are loaded onto nascent class II MHC molecules via the classical DM-dependent pathway.
Prediction of Survival in Multiple Myeloma Based on Gene Expression Profiles Reveals Cell Cycle and Chromosomal Instability Signatures in High-Risk Patients and Hyperdiploid Signatures in Low-Risk Patients: A Study of the Intergroupe Francophone du Myélome
Authors: Decaux Olivier , Lodé Laurence , Magrangeas Florence , Charbonnel Catherine , Gouraud Wilfried , Jézéquel Pascal , Attal Michel , Harousseau Jean-Luc , Moreau Philippe , Bataille Régis , Campion Loïc , Avet-Loiseau Hervé , Minvielle Stéphane 
Published: July 2008

Purpose Survival of patients with multiple myeloma is highly heterogeneous, from periods of a few weeks to more than 10 years. We used gene expression profiles of myeloma cells obtained at diagnosis to identify broadly applicable prognostic markers. Patients and Methods In a training set of 182 patients, we used supervised methods to identify individual genes associated with length of survival. A survival model was built from these genes. The validity of our model was assessed in our test set of 68 patients and in three independent cohorts comprising 853 patients with multiple myeloma. Results The 15 strongest genes associated with the length of survival were used to calculate a risk score and to stratify patients into low-risk and high-risk groups. The survival-predictor score was significantly associated with survival in both the training and test sets and in the external validation cohorts. The Kaplan-Meier estimates of rates of survival at 3 years were 90.5% (95% CI, 85.6% to 95.3%) and 47.4% (95% CI, 33.5% to 60.1%), respectively, in our patients having a low risk or high risk independently of traditional prognostic factors. High-risk patients constituted a homogeneous biologic entity characterized by the overexpression of genes involved in cell cycle progression and its surveillance, whereas low-risk patients were heterogeneous and displayed hyperdiploid signatures. Conclusion Gene expression–based survival prediction and molecular features associated with high-risk patients may be useful for developing prognostic markers and may provide basis to treat these patients with new targeted antimitotics.