bluuebunny/crossref_metadata_2025_split huggingface dataset:
Socioeconomic inequality of cancer mortality in the United States: a spatial data mining approach
Authors: Vinnakota Srinivas , Lam Nina SN 
Published: February 2006

Abstract

Background
The objective of this study was to demonstrate the use of an association rule mining approach to discover associations between selected socioeconomic variables and the four most leading causes of cancer mortality in the United States. An association rule mining algorithm was applied to extract associations between the 1988–1992 cancer mortality rates for colorectal, lung, breast, and prostate cancers defined at the Health Service Area level and selected socioeconomic variables from the 1990 United States census. Geographic information system technology was used to integrate these data which were defined at different spatial resolutions, and to visualize and analyze the results from the association rule mining process.

Results
Health Service Areas with high rates of low education, high unemployment, and low paying jobs were found to associate with higher rates of cancer mortality.

Conclusion
Association rule mining with geographic information technology helps reveal the spatial patterns of socioeconomic inequality in cancer mortality in the United States and identify regions that need further attention.
Complete probabilistic analysis of RNA shapes
Authors: Voß Björn , Giegerich Robert , Rehmsmeier Marc 
Published: February 2006

Abstract

Background

Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived.

Results

In this paper we extend the approach of abstract shape analysis. We show how to compute the accumulated probabilities of all structures that share the same shape. While this implies a complete (non-heuristic) analysis of the folding space, the computational effort depends only on the size of the shape space, which is much smaller. This approach has been integrated into the tool RNAshapes, and we apply it to various RNAs.

Conclusion

Analyses of conformational switches show the existence of two shapes with probabilities approximately

2
3

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vs.

1
3

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, whereas the analysis of a microRNA precursor reveals one shape with a probability near to 1.0. Furthermore, it is shown that a shape can outperform an energetically more favourable one by achieving a higher probability. From these results, and the fact that we use a complete and exact analysis of the folding space, we conclude that this approach opens up new and promising routes for investigating and understanding RNA secondary structure.
A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies
Authors: Ribba Benjamin , Colin Thierry , Schnell Santiago 
Published: February 2006

Abstract

Background
Radiotherapy outcomes are usually predicted using the Linear Quadratic model. However, this model does not integrate complex features of tumor growth, in particular cell cycle regulation.

Methods
In this paper, we propose a multiscale model of cancer growth based on the genetic and molecular features of the evolution of colorectal cancer. The model includes key genes, cellular kinetics, tissue dynamics, macroscopic tumor evolution and radiosensitivity dependence on the cell cycle phase. We investigate the role of gene-dependent cell cycle regulation in the response of tumors to therapeutic irradiation protocols.

Results
Simulation results emphasize the importance of tumor tissue features and the need to consider regulating factors such as hypoxia, as well as tumor geometry and tissue dynamics, in predicting and improving radiotherapeutic efficacy.

Conclusion
This model provides insight into the coupling of complex biological processes, which leads to a better understanding of oncogenesis. This will hopefully lead to improved irradiation therapy.
Determinants of bone mass and bone size in a large cohort of physically active young adult men
Authors: Ruffing JA , Cosman F , Zion M , Tendy Susan , Garrett P , Lindsay R , Nieves JW 
Published: February 2006

Abstract
The determinants of bone mineral density (BMD) at multiple sites were examined in a fit college population. Subjects were 755 males (mean age = 18.7 years) entering the United States Military Academy. A questionnaire assessed exercise frequency and milk, caffeine, and alcohol consumption and tobacco use. Academy staff measured height, weight, and fitness. Calcaneal BMD was measured by peripheral dual-energy x-ray absorptiometry (pDXA). Peripheral-quantitative computed tomography (pQCT) was used to measure tibial mineral content, circumference and cortical thickness. Spine and hip BMD were measured by DXA in a subset (n = 159). Mean BMD at all sites was approximately one standard deviation above young normal (p < 0.05). African Americans had significantly higher hip, spine and heel BMD and greater tibial mineral content and cortical thickness than Caucasians and Asians. In Caucasians (n = 653), weight was a significant determinant of BMD at every skeletal site. Prior exercise levels and milk intake positively related to bone density and size, while caffeine had a negative impact. There was an apparent interaction between milk and exercise in BMD at the heel, spine, hip and tibial mineral content and cortical thickness. Our data confirm the importance of race, body size, milk intake and duration of weekly exercise as determinants of BMD and bone size.
Effect of food deprivation and hormones of glucose homeostasis on the acetyl CoA carboxylase activity in mouse brain: a potential role of acc in the regulation of energy balance
Authors: Karami Kristophe J , Coppola John , Krishnamurthy Karthik , Llanos Domingo J , Mukherjee Amrita , Venkatachalam KV 
Published: February 2006

Abstract
We studied the regulation of brain acetyl CoA carboxylase (ACC) activity during food deprivation and under the influence of hormones of glucose homeostasis: glucagon and insulin. Mice were deprived of food and water for time periods of 1, 3, 6, 9, 12 and 24 hours and were then allowed to re-feed for 5, 30 and 60 minutes. Mice that were deprived for up to 6 h, and then re-fed for 60 min, consumed the same amount of food compared to the ad libitum (control) animals. However, after 9 h of deprivation, mice consumed only 50% of food present even after 1 h of re-feeding, compared to the controls. The ACC activity was measured in the whole mouse brain of controls and after 1, 3, 6, 9, 12, and 24 h of food deprivation. Brain extracts assayed from control mice expressed an ACC activity of 0.988 ± 0.158 fmol/min/mg tissue without citrate and 0.941 ± 0.175 fmol/min/mg tissue with citrate. After 1 h of food deprivation, the total ACC activity without citrate decreased to 0.575 ± 0.087 fmol/min/mg and in the presence of citrate, 0.703 ± 0.036 fmol/min/mg activity was measured. The citrate-dependent ACC activity decreased over time, with only 0.478 ± 0.117 fmol/min/mg of activity remaining after 24 h. Intraperitoneal (i.p.) injections of insulin, glucagon and phosphate buffered saline (PBS) were performed and whole brain ACC activity measured. After hormone administration, there were no significant differences in ACC activity in the presence of citrate. However, in the absence of citrate, there was a significant 20% decrease in ACC activity with glucagon (1.36 ± 0.09 fmol/min/mg) and a 33% increase with insulin (2.49 ± 0.11 fmol/min/mg) injections compared to PBS controls (1.67 ± 0.08 fmol/min/mg). Neuropeptide Y (NPY) levels of corresponding brain extracts were measured by ELISA (OD) using anti-NPY antibody and showed an 18% decrease upon insulin injection (0.093 ± 0.019) and a 50% increase upon glucagon injection (0.226 ± 0.084) as compared to controls injected with PBS (0.114 ± 0.040). Thus, we postulate that the changes in ACC levels under metabolic conditions would result in a fluctuation of malonyl CoA levels, and subsequent modulation of NPY levels and downstream signaling.
Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
Authors: Lindberg Johan , af Klint Erik , Ulfgren Ann-Kristin , Stark André , Andersson Tove , Nilsson Peter , Klareskog Lars , Lundeberg Joakim 
Published: February 2006

AbstractIn recent years microarray technology has been used increasingly to acquire knowledge about the pathogenic processes involved in rheumatoid arthritis. The present study investigated variations in gene expression in synovial tissues within and between patients with rheumatoid arthritis. This was done by applying microarray technology on multiple synovial biopsies obtained from the same knee joints. In this way the relative levels of intra-patient and inter-patient variation could be assessed. The biopsies were obtained from 13 different patients: 7 by orthopedic surgery and 6 by rheumatic arthroscopy. The data show that levels of heterogeneity varied substantially between the biopsies, because the number of genes found to be differentially expressed between pairs of biopsies from the same knee ranged from 6 to 2,133. Both arthroscopic and orthopedic biopsies were examined, allowing us to compare the two sampling methods. We found that the average number of differentially expressed genes between biopsies from the same patient was about three times larger in orthopedic than in arthroscopic biopsies. Using a parallel analysis of the tissues by immunohistochemistry, we also identified orthopedic biopsies that were unsuitable for gene expression analysis of synovial inflammation due to sampling of non-inflamed parts of the tissue. Removing these biopsies reduced the average number of differentially expressed genes between the orthopedic biopsies from 455 to 171, in comparison with 143 for the arthroscopic biopsies. Hierarchical clustering analysis showed that the remaining orthopedic and arthroscopic biopsies had gene expression signatures that were unique for each patient, apparently reflecting patient variation rather than tissue heterogeneity. Subsets of genes found to vary between biopsies were investigated for overrepresentation of biological processes by using gene ontology. This revealed representative 'themes' likely to vary between synovial biopsies affected by inflammatory disease.
Medical Emergency Team syndromes and an approach to their management
Authors: Jones Daryl , Duke Graeme , Green John , Briedis Juris , Bellomo Rinaldo , Casamento Andrew , Kattula Andrea , Way Margaret 
Published: February 2006

Abstract
Introduction
Most literature on the medical emergency team (MET) relates to its effects on patient outcome. Less information exists on the most common causes of MET calls or on possible approaches to their management.

Methods
We reviewed the calling criteria and clinical causes of 400 MET calls in a teaching hospital. We propose a set of minimum standards for managing a MET review and developed an approach for managing common problems encountered during MET calls.

Results
The underlying reasons for initiating MET calls were hypoxia (41%), hypotension (28%), altered conscious state (23%), tachycardia (19%), increased respiratory rate (14%) and oliguria (8%). Infection, pulmonary oedema, and arrhythmias featured as prominent causes of all triggers for MET calls. The proposed minimum requirements for managing a MET review included determining the cause of the deterioration, documenting the events surrounding the MET, establishing a medical plan and ongoing medical follow-up, and discussing the case with the intensivist if certain criteria were fulfilled. A systematic approach to managing episodes of MET review was developed based on the acronym 'A to G': a sk and a ssess; b egin b asic investigations and resuscitation, c all for help if needed, d iscuss, d ecide, and d ocument, e xplain aetiology and management, f ollow-up, and g raciously thank staff. This approach was then adapted to provide a management plan for episodes of tachycardia, hypotension, hypoxia and dyspnoea, reduced urinary output, and altered conscious state.

Conclusion
A suggested approach permits audit and standardization of the management of MET calls and provides an educational framework for the management of acutely unwell ward patients. Further evaluation and validation of the approach are required.
Predicting genes for orphan metabolic activities using phylogenetic profiles
Authors: Chen Lifeng , Vitkup Dennis 
Published: February 2006

AbstractHomology-based methods fail to assign genes to many metabolic activities present in sequenced organisms. To suggest genes for these orphan activities we developed a novel method that efficiently combines local structure of a metabolic network with phylogenetic profiles. We validated our method using known metabolic genes in Saccharomyces cerevisiae and Escherichia coli. We show that our method should be easily transferable to other organisms, and that it is robust to errors in incomplete metabolic networks.
Global analysis of X-chromosome dosage compensation
Authors: Gupta Vaijayanti , Parisi Michael , Sturgill David , Nuttall Rachel , Doctolero Michael , Dudko Olga K , Malley James D , Eastman P Scott , Oliver Brian 
Published: February 2006

Abstract
Background
Drosophila melanogaster females have two X chromosomes and two autosome sets (XX;AA), while males have a single X chromosome and two autosome sets (X;AA). Drosophila male somatic cells compensate for a single copy of the X chromosome by deploying male-specific-lethal (MSL) complexes that increase transcription from the X chromosome. Male germ cells lack MSL complexes, indicating that either germline X-chromosome dosage compensation is MSL-independent, or that germ cells do not carry out dosage compensation.

Results
To investigate whether dosage compensation occurs in germ cells, we directly assayed X-chromosome transcripts using DNA microarrays and show equivalent expression in XX;AA and X;AA germline tissues. In X;AA germ cells, expression from the single X chromosome is about twice that of a single autosome. This mechanism ensures balanced X-chromosome expression between the sexes and, more importantly, it ensures balanced expression between the single X chromosome and the autosome set. Oddly, the inactivation of an X chromosome in mammalian females reduces the effective X-chromosome dose and means that females face the same X-chromosome transcript deficiency as males. Contrary to most current dosage-compensation models, we also show increased X-chromosome expression in X;AA and XX;AA somatic cells of Caenorhabditis elegans and mice.

Conclusion
Drosophila germ cells compensate for X-chromosome dose. This occurs by equilibrating X-chromosome and autosome expression in X;AA cells. Increased expression of the X chromosome in X;AA individuals appears to be phylogenetically conserved.
Peroxisome Proliferator-Activated Receptor γ Recruits the Positive Transcription Elongation Factor b Complex to Activate Transcription and Promote Adipogenesis
Authors: Iankova Irena , Petersen Rasmus K. , Annicotte Jean-Sébastien , Chavey Carine , Hansen Jacob B. , Kratchmarova Irina , Sarruf David , Benkirane Monsef , Kristiansen Karsten , Fajas Lluis 
Published: February 2006

AbstractPositive transcription elongation factor b (P-TEFb) phosphorylates the C-terminal domain of RNA polymerase II, facilitating transcriptional elongation. In addition to its participation in general transcription, P-TEFb is recruited to specific promoters by some transcription factors such as c-Myc or MyoD. The P-TEFb complex is composed of a cyclin-dependent kinase (cdk9) subunit and a regulatory partner (cyclin T1, cyclin T2, or cyclin K). Because cdk9 has been shown to participate in differentiation processes, such as muscle cell differentiation, we studied a possible role of cdk9 in adipogenesis. In this study we show that the expression of the cdk9 p55 isoform is highly regulated during 3T3-L1 adipocyte differentiation at RNA and protein levels. Furthermore, cdk9, as well as cyclin T1 and cyclin T2, shows differences in nuclear localization at distinct stages of adipogenesis. Overexpression of cdk9 increases the adipogenic potential of 3T3-L1 cells, whereas inhibition of cdk9 by specific cdk inhibitors, and dominant-negative cdk9 mutant impairs adipogenesis. We show that the positive effects of cdk9 on the differentiation of 3T3-L1 cells are mediated by a direct interaction with and phosphorylation of peroxisome proliferator-activated receptor γ (PPARγ), which is the master regulator of this process, on the promoter of PPARγ target genes. PPARγ-cdk9 interaction results in increased transcriptional activity of PPARγ and therefore increased adipogenesis.
Estrogen-Related Receptors-Stimulated Monoamine Oxidase B Promoter Activity Is Down-Regulated by Estrogen Receptors
Authors: Zhang Zhiping , Chen Kevin , Shih Jean C. , Teng Christina T. 
Published: February 2006

AbstractAlthough there are studies published about the neuroprotective effect of estrogen, little is known about the mechanisms and cellular targets of the hormone. Recent reports demonstrate that estrogen down-regulates the expression of monoamine oxidase A and B (MAO-A and MAO-B) in the hypothalamus of the Macaques monkey, both of which are key isoenzymes in the neurotransmitter degradation pathway. Additionally, estrogen-related receptor α (ERRα) up-regulates MAO-B gene expression in breast cancer cells. ERRα recognizes a variety of estrogen response elements and shares many target genes and coactivators with estrogen receptor α (ERα). In this study, we investigate the interplay of ERs and ERRs in the regulation of MAO-B promoter activity. We demonstrate that ERRα and ERRγ up-regulate MAO-B gene activity, whereas ERα and ERβ decrease stimulation in both a ligand-dependent and -independent manner. Ectopically expressed ERRα and ERRγ stimulate the expression of MAO-B mRNA and protein as well as increase the MAO-B enzymatic activity in ER-negative HeLa cells. The ability of ERRs to stimulate MAO-B promoter activity was reduced in ER-positive MCF-7 and T47D cells. Several AGGTCA motifs of the MAO-B promoter are responsible for up-regulation by ERRs. Interestingly, ERα or ERβ alone have no effect on MAO-B promoter activity but can down-regulate the activation function of ERRs, whereas glucocorticoid receptor does not. By using chromatin immunoprecipitation assay, we demonstrate that ERs compete with ERRs for binding to the MAO-B promoter at selective AGGTCA motifs, thereby changing the chromatin status and cofactor recruitment to a repressed state. These studies provide new insight into the relationship between ERα, ERβ, ERRα, and ERRγ in modulation of MAO-B gene activity.
Bowel Perforation Caused by Peritoneal Shunt Catheters:Diagnosis and Treatment
Authors: Vinchon Matthieu , Baroncini Marc , Laurent Thines , Patrick Dhellemmes 
Published: February 2006

Abstract

OBJECTIVE:
The peritoneum is the preferred site for insertion of shunts used for the treatment of hydrocephalus. Bowel perforation by peritoneal catheters (BPPC) is a rare but devastating complication. Its pathophysiology, diagnosis, and treatment are debated.

METHODS:
Retrospective review of cases of BPPC in a series of 1956 patients having a peritoneal catheter followed up for a mean duration of 10.0 years.

RESULTS:
Nineteen observations of BPPC, representing 1.0% of the total series. Nine of 19 patients were nonambulatory, and nine of 19 had a previous history of meningeal infection. At the time of diagnosis, only three of the 19 patients had anal extrusion of the catheter, 14 had fever, nine had abdominal signs and symptoms, and six had cutaneous signs of infection. Radiological investigations were often negative or inconclusive. In seven of the patients, the initial diagnosis was shunt failure, and BPPC was diagnosed only during shunt revision. Once the correct diagnosis was made, the treatment was total shunt removal, external drainage, and antibiotic therapy for 2 weeks. Three patients, all severely impaired before BPPC, died, one of meningeal sepsis, the others of multiorgan failure related to spastic tetraparesis. Three were considered shunt-independent, two had a ventriculoatrial shunt, and the others had a new shunt with a peritoneal catheter without complication.

CONCLUSION:
BPPC is a neurosurgical emergency. Anal extrusion is present in only a minority of patients; the diagnosis of BPPC is often difficult, delayed, and its incidence is likely underestimated. The majority of patients can be treated with a new peritoneal shunt after cure of the infection.
Experience with Microelectrode Guided Subthalamic Nucleus Deep Brain Stimulation
Authors: Amirnovin Ramin , Williams Ziv M. , Cosgrove G. Rees , Eskandar Emad N. 
Published: February 2006

Abstract

OBJECTIVE:
Subthalamic deep brain stimulation (DBS) has rapidly become the standard surgical therapy for medically refractory Parkinson disease. However, in spite of its wide acceptance, there is considerable variability in the technical approach. This study details our technique and experience in performing microelectrode recording (MER) guided subthalamic nucleus (STN) DBS in the treatment of Parkinson disease.

METHODS:
Forty patients underwent surgery for the implantation of 70 STN DBS electrodes. Stereotactic localization was performed using a combination of magnetic resonance and computed tomographic imaging. We used an array of three microelectrodes, separated by 2 mm, for physiological localization of the STN. The final location was selected based on MER and macrostimulation through the DBS electrode.

RESULTS:
The trajectory selected for the DBS electrode had an average pass through the STN of 5.6 ± 0.4 mm on the left and 5.7 ± 0.4 mm on the right. The predicted location was used in 42% of the cases but was modified by MER in the remaining 58%. Patients were typically discharged on the second postoperative day. Eighty-five percent of patients were sent home, 13% required short-term rehabilitation, and one patient required long-term nursing services. Seven complications occurred over 4 years. Four patients suffered small hemorrhages, one patient experienced a lead migration, one developed an infection of the pulse generator, and one patient suffered from a superficial cranial infection.

CONCLUSION:
Simultaneous bilateral MER-guided subthalamic DBS is a relatively safe and well-tolerated procedure. MER plays an important role in optimal localization of the DBS electrodes.