bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMRT in oral cavity cancer
Authors: Studer Gabriela , Zwahlen Roger A , Graetz Klaus W , Davis Bernard J , Glanzmann Christoph 
Published: May 2007

Abstract
Background
Except for early T1,2 N0 stages, the prognosis for patients with oral cavity cancer (OCC) is reported to be worse than for carcinoma in other sites of the head and neck (HNC). The aim of this work was to assess disease outcome in OCC following IMRT.
Between January 2002 and January 2007, 346 HNC patients have been treated with curative intensity modulated radiation therapy (IMRT) at the Department of Radiation Oncology, University Hospital Zurich. Fifty eight of these (16%) were referred for postoperative (28) or definitive (30) radiation therapy of OCC.
40 of the 58 OCC patients (69%) presented with locally advanced T3/4 or recurred lesions. Doses between 60 and 70 Gy were applied, combined with simultaneous cisplatin based chemotherapy in 78%. Outcome analyses were performed using Kaplan Meier curves.
In addition, comparisons were performed between this IMRT OCC cohort and historic in-house cohorts of 33 conventionally irradiated (3DCRT) and 30 surgery only patients treated over the last 10 years.

Results
OCC patients treated with postoperative IMRT showed the highest local control (LC) rate of all assessed treatment sequence subgroups (92% LC at 2 years). Historic postoperative 3DCRT patients and patients treated with surgery alone reached LC rates of ~70–80%. Definitively irradiated patients revealed poorest LC rates with ~30 and 40% following 3DCRT and IMRT, respectively.
T1 stage resulted in an expectedly significantly higher LC rate (95%, n = 19, p < 0.05) than T2-4 and recurred stages (LC ~50–60%, n = 102).
Analyses according to the diagnosis revealed significantly lower LC in OCC following definitive IMRT than that in pharyngeal tumors treated with definitive IMRT in the same time period (43% vs 82% at 2 years, p < 0.0001), while the LC rate of OCC following postoperative IMRT was as high as in pharyngeal tumors treated with postoperative IMRT (>90% at 2 years).

Conclusion
Postoperative IMRT of OCC resulted in the highest local control rate of the assessed treatment subgroups. In conclusion, generous indication for IMRT following surgical treatment is recommended in OCC cases with unfavourable features like tight surgical margin, nodal involvement, primary tumor stage >T1N0, or already recurred disease, respectively.
Loco-regional outcome of OCC following definitive IMRT remained unsatisfactory, comparable to that following definitive 3DCRT.
Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12
Authors: Sun Jingjun , Tuncay Kagan , Haidar Alaa Abi , Ensman Lisa , Stanley Frank , Trelinski Michael , Ortoleva Peter 
Published: May 2007

Abstract
Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and phylogenic similarity to accurately discover TRNs and apply the method to E. coli K12. The approach can easily be extended to include other methodologies. Although gene ontology and phylogenic similarity have been used in the context of gene-gene networks, we show that more information can be extracted when gene-gene scores are transformed to gene-transcription factor (TF) scores using a preliminary TRN. This seems to be preferable over the construction of gene-gene interaction networks in light of the observed fact that gene expression and activity of a TF made of a component encoded by that gene is often out of phase. TRND multi-method integration is found to be facilitated by the use of a Bayesian framework for each method derived from its individual scoring measure and a training set of gene/TF regulatory interactions. The TRNs we construct are in better agreement with microarray data. The number of gene/TF interactions we discover is actually double that of existing networks.
Distal thoracic oesophageal perforation secondary to blunt trauma: Case report
Authors: Strauss Dirk C , Tandon Ruchi , Mason Robert C 
Published: May 2007

AbstractBackgroundTraumatic perforation of the distal oesophagus due to blunt trauma is a very rare condition and is still associated with a significant morbidity and mortality. This is further exacerbated by delayed diagnosis and management as symptoms and signs are often masked by or ascribed to more common blunt thoracic injuries.Case reportWe present a case of a distal oesophageal perforation, secondary to a fall from a third storey window, which was masked by concomitant thoracic injuries and missed on both computed tomography imaging and laparotomy. The delay in his diagnosis significantly worsened the patient's recovery by allowing the development of an overwhelming chest sepsis that contributed to his death.ConclusionEarly identification of an intrathoracic oesophageal perforation requires deliberate consideration and is essential to ensure a favorable outcome. Treatment should be individualised taking into account the nature of the oesophageal defect, time elapsed from injury and the patient's general condition.
Duhuo Jisheng Tang for treating osteoarthritis of the knee: a prospective clinical observation
Authors: Lai Jung-Nien , Chen Huey-Jeng , Chen Chao-Chung , Lin Jer-Huei , Hwang Jing-Shiang , Wang Jung-Der 
Published: May 2007

Abstract

Background
Little scientific evidence supports the efficacy of herbal medicines in the treatment of degenerative arthritis of the knee. The purpose of this study is to evaluate both the efficacy and safety of a finished Chinese herbal preparation Duhuo Jisheng Tang (DJT) in reducing symptoms of degenerative osteoarthritis of the knee.

Methods
A prospective follow-up study was carried out in two hospitals in Taipei between April and October 2005. Sixty-eight osteoarthritis patients, with symptoms diagnosed by radiologists, received DJT at a rate of 2.5 g, twice daily for four weeks. Baseline scores were measured on the Western Ontario and McMaster Universities Osteoarthritis (WOMAC) index, followed by further measures at the end of weeks 1, 2 and 4. The World Health Organization Quality of Life (WHOQOL) assessment was undertaken as a secondary outcome, with pattern identification questionnaires being adopted. Regression models were constructed to explore the score differences between the baseline and at weeks 2 and 4 by various determinants including age, gender, body mass index (BMI), severity at baseline, use of rescue medication, aversion to cold and flaccidity of the lower back and knees.

Results
Among the 68 participants, there were statistically significant reductions in the WOMAC index scores for pain, stiffness and physical functioning in the second and fourth weeks, with effects first appearing during week 2. By week 4, the mean WOMAC index scores had fallen from 22.2 (± 19.2) to 16.1 (± 16.2) for pain, from 28.1 (± 24.9) to 18.5 (± 20.3) for stiffness, and from 22.6 (± 18.0) to 18.2 (± 17.8) for physical functioning, while the global score for pain under the visual analogue scale (VAS) was reduced from 38.7 (± 21.5) to 27.8 (± 19.8).

Conclusion
In the treatment of degenerative osteoarthritis of the knee, a 4-week therapy with the Chinese herbal preparation DJT reduced pain and stiffness and improved physical functioning, but it was less effective in treating flaccidity and aversion to cold.
Cirrhotic cardiomyopathy
Authors: Baik Soon Koo , Fouad Tamer R , Lee Samuel S 
Published: May 2007

Abstract
Cirrhotic cardiomyopathy is the term used to describe a constellation of features indicative of abnormal heart structure and function in patients with cirrhosis. These include systolic and diastolic dysfunction, electrophysiological changes, and macroscopic and microscopic structural changes. The prevalence of cirrhotic cardiomyopathy remains unknown at present, mostly because the disease is generally latent and shows itself when the patient is subjected to stress such as exercise, drugs, hemorrhage and surgery. The main clinical features of cirrhotic cardiomyopathy include baseline increased cardiac output, attenuated systolic contraction or diastolic relaxation in response to physiologic, pharmacologic and surgical stress, and electrical conductance abnormalities (prolonged QT interval). In the majority of cases, diastolic dysfunction precedes systolic dysfunction, which tends to manifest only under conditions of stress. Generally, cirrhotic cardiomyopathy with overt severe heart failure is rare. Major stresses on the cardiovascular system such as liver transplantation, infections and insertion of transjugular intrahepatic portosystemic stent-shunts (TIPS) can unmask the presence of cirrhotic cardiomyopathy and thereby convert latent to overt heart failure. Cirrhotic cardiomyopathy may also contribute to the pathogenesis of hepatorenal syndrome. Pathogenic mechanisms of cirrhotic cardiomyopathy are multiple and include abnormal membrane biophysical characteristics, impaired β-adrenergic receptor signal transduction and increased activity of negative-inotropic pathways mediated by cGMP. Diagnosis and differential diagnosis require a careful assessment of patient history probing for excessive alcohol, physical examination for signs of hypertension such as retinal vascular changes, and appropriate diagnostic tests such as exercise stress electrocardiography, nuclear heart scans and coronary angiography. Current management recommendations include empirical, nonspecific and mainly supportive measures. The exact prognosis remains unclear. The extent of cirrhotic cardiomyopathy generally correlates to the degree of liver insufficiency. Reversibility is possible (either pharmacological or after liver transplantation), but further studies are needed.
Differential expression of interferon responsive genes in rodent models of transmissible spongiform encephalopathy disease
Authors: Stobart Michael J , Parchaliuk Debra , Simon Sharon LR , LeMaistre Jillian , Lazar Jozef , Rubenstein Richard , Knox J David 
Published: May 2007

Abstract

Background
The pathological hallmarks of transmissible spongiform encephalopathy (TSE) diseases are the deposition of a misfolded form of a host-encoded protein (PrPres), marked astrocytosis, microglial activation and spongiosis. The development of powerful gene based technologies has permitted increased levels of pro-inflammatory cytokines to be demonstrated. However, due to the use of assays of differing sensitivities and typically the analysis of a single model system it remained unclear whether this was a general feature of these diseases or to what extent different model systems and routes of infection influenced the relative levels of expression. Similarly, it was not clear whether the elevated levels of cytokines observed in the brain were accompanied by similar increases in other tissues that accumulate PrPres, such as the spleen.

Results
The level of expression of the three interferon responsive genes, Eif2ak2, 2'5'-OAS, and Mx2, was measured in the brains of Syrian hamsters infected with scrapie 263K, VM mice infected with bovine spongiform encephalopathy and C57BL/6 mice infected with the scrapie strain ME7. Glial fibrillary acidic expression confirmed the occurrence of astrocytosis in all models. When infected intracranially all three models showed a similar pattern of increased expression of the interferon responsive genes at the onset of clinical symptoms. At the terminal stage of the disease the level and pattern of expression of the three genes was mostly unchanged in the mouse models. In contrast, in hamsters infected by either the intracranial or intraperitoneal routes, both the level of expression and the expression of the three genes relative to one another was altered. Increased interferon responsive gene expression was not observed in a transgenic mouse model of Alzheimer's disease or the spleens of C57BL/6 mice infected with ME7. Concurrent increases in TNFα, TNFR1, Fas/ApoI receptor, and caspase 8 expression in ME7 infected C57BL/6 mice were observed.

Conclusion
The identification of increased interferon responsive gene expression in the brains of three rodent models of TSE disease at two different stages of disease progression suggest that this may be a general feature of the disease in rodents. In addition, it was determined that the increased interferon responsive gene expression was confined to the CNS and that the TSE model system and the route of infection influenced the pattern and extent of the increased expression. The concurrent increase in initiators of Eif2ak2 mediated apoptotic pathways in C57BL/6 mice infected with ME7 suggested one mechanism by which increased interferon responsive gene expression may enhance disease progression.
Lack of α-synuclein increases amyloid plaque accumulation in a transgenic mouse model of Alzheimer's disease
Authors: Kallhoff Verena , Peethumnongsin Erica , Zheng Hui 
Published: May 2007

Abstract
α-synuclein is a small soluble, cytosolic protein which associates with vesicular membranes. It is a component of intracellular Lewy bodies present in Parkinson's disease and a subset of Alzheimer's disease (AD). In addition, early studies identified a fragment of α-synuclein in the amyloid plaques of AD patients. Hypothesizing that α-synuclein might modify the AD pathogenic process, we crossed the Tg2576 strain of APP transgenic mice onto an α-synuclein knockout background to determine the effects of α-synuclein on Aβ production and plaque deposition. We found that α-synuclein deficiency does not affect the Aβ levels, nor does it alter the age of onset of plaque pathology. To our surprise, however, loss of α-synuclein leads to a significant increase in plaque load in all areas of the forebrain at 18 months of age. This is associated with an increase in another synaptic protein, synaptophysin. We thus conclude that α-synuclein is not involved in seeding of the plaques, but rather suppresses the progression of plaque pathology at advanced stages.
Apolipoprotein E levels in cerebrospinal fluid and the effects of ABCA1polymorphisms
Authors: Wahrle Suzanne E , Shah Aarti R , Fagan Anne M , Smemo Scott , Kauwe John SK , Grupe Andrew , Hinrichs Anthony , Mayo Kevin , Jiang Hong , Thal Leon J , Goate Alison M , Holtzman David M 
Published: May 2007

Abstract

Background
Animal studies suggest that brain apolipoprotein E (apoE) levels influence amyloid-β (Aβ) deposition and thus risk for Alzheimer's disease (AD). We have previously demonstrated that deletion of the ATP-binding cassette A1 transporter (ABCA1) in mice causes dramatic reductions in brain and cerebrospinal fluid (CSF) apoE levels and lipidation. To examine whether polymorphisms in ABCA1 affect CSF apoE levels in humans, we measured apoE in CSF taken from 168 subjects who were 43 to 91 years old and were either cognitively normal or who had mild AD. We then genotyped the subjects for ten previously identified ABCA1 single nucleotide polymorphisms (SNPs).

Results
In all subjects, the mean CSF apoE level was 9.09 μg/ml with a standard deviation of 2.70 μg/ml. Levels of apoE in CSF samples taken from the same individual two weeks apart were strongly correlated (r2 = 0.93, p < 0.01). In contrast, CSF apoE levels in different individuals varied widely (coefficient of variation = 46%). CSF apoE levels did not vary according to AD status, APOE genotype, gender or race. Average apoE levels increased with age by ~0.5 μg/ml per 10 years (r2 = 0.05, p = 0.003). We found no significant associations between CSF apoE levels and the ten ABCA1 SNPs we genotyped. Moreover, in a separate sample of 1225 AD cases and 1431 controls, we found no association between the ABCA1 SNP rs2230806 and AD as has been previously reported.

Conclusion
We found that CSF apoE levels vary widely between individuals, but are stable within individuals over a two-week interval. AD status, APOE genotype, gender and race do not affect CSF apoE levels, but average CSF apoE levels increase with age. Given the lack of association between CSF apoE levels and genotypes for the ABCA1 SNPs we examined, either these SNPs do not affect ABCA1 function or if they do, they do not have strong effects in the CNS. Finally, we find no evidence for an association between the ABCA1 SNP rs2230806 and AD in a large sample set.
Caries in the infundibulum of the second upper premolar tooth in the horse
Authors: Lundström Torbjörn S , Dahlén Gunnar G , Wattle Ove S 
Published: May 2007

Abstract

Background
Swedish equine dental practices have empirically found that the prevalence of infundibular caries as a primary disorder in the first permanent premolar teeth (P2) of the horse upper jaw has increased during the last 10 years. A previously unknown bacterial species, Streptococcus devriesei (CCUG 47155T), which is related to Streptococcus mutans, has recently been isolated from these carious lesions. To understand the aetiology of caries in horses, it is essential to elucidate the relationship between S. devriesei and P2 infundibular caries.

Methods
The anterior infundibulum of maxillary P2, or the occlusal surface at the site of the infundibulum, in 117 horses and ponies, 77 with and 40 without caries in this tooth, was sampled for bacteriological analyses between 1990 and 2004. Samples were transported in VMGA III medium and then inoculated onto MSB agar. The approximate number of bacteria was counted in each sample and the isolates were characterised biochemically, using a commercial kit.

Results
All 50 samples taken from carious lesions after 2002 were positive for an S. mutans-like strain, i.e. S. devriesei. The bacteria were also found in four of the control animals, but were much less numerous than in samples from caries-affected horses. None of the swabs taken prior to 2002 were positive for this bacteria.

Conclusion
Our results demonstrate that S. devriesei can colonise the infundibulum of P2 of the horse upper jaw, which can be fatal for the dental tissue. We conclude that S. devriesei is strongly associated with P2 caries in horses.
HitKeeper, a generic software package for hit list management
Authors: Hau Jörg , Muller Michael , Pagni Marco 
Published: May 2007

Abstract

Background
The automated annotation of biological sequences (protein, DNA) relies on the computation of hits (predicted features) on the sequences using various algorithms. Public databases of biological sequences provide a wealth of biological "knowledge", for example manually validated annotations (features) that are located on the sequences, but mining the sequence annotations and especially the predicted and curated features requires dedicated tools. Due to the heterogeneity and diversity of the biological information, it is difficult to handle redundancy, frequent updates, taxonomic information and "private" data together with computational algorithms in a common workflow.

Results
We present HitKeeper, a software package that controls the fully automatic handling of multiple biological databases and of hit list calculations on a large scale. The software implements an asynchronous update system that introduces updates and computes hits as soon as new data become available. A query interface enables the user to search sequences by specifying constraints, such as retrieving sequences that contain specific motifs, or a defined arrangement of motifs ("metamotifs"), or filtering based on the taxonomic classification of a sequence.

Conclusion
The software provides a generic and modular framework to handle the redundancy and incremental updates of biological databases, and an original query language. It is published under the terms and conditions of version 2 of the GNU Public License and available at http://hitkeeper.sourceforge.net.
Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
Authors: Çakır Tunahan , Kırdar Betül , Önsan Zİlsen , Ülgen Kutlu Ö , Nielsen Jens 
Published: May 2007

Abstract

Background
Control effective flux (CEF) of a reaction is the weighted sum of all fluxes through that reaction, derived from elementary flux modes (EFM) of a metabolic network. Change in CEFs under different environmental conditions has earlier been proven to be correlated with the corresponding changes in the transcriptome. Here we use this to investigate the degree of transcriptional regulation of fluxes in the metabolism of Saccharomyces cerevisiae. We do this by quantifying correlations between changes in CEFs and changes in transcript levels for shifts in carbon source, i.e. between the fermentative carbon source glucose and nonfermentative carbon sources like ethanol, acetate, and lactate. The CEF analysis is based on a simple stoichiometric model that includes reactions of the central carbon metabolism and the amino acid metabolism.

Results
The effect of the carbon shift on the metabolic fluxes was investigated for both batch and chemostat cultures. For growth on glucose in batch (respiro-fermentative) cultures, EFMs with no by-product formation were removed from the analysis of the CEFs, whereas those including any by-products (ethanol, glycerol, acetate, succinate) were omitted in the analysis of growth on glucose in chemostat (respiratory) cultures. This resulted in improved correlations between CEF changes and transcript levels. A regression correlation coefficient of 0.60 was obtained between CEF changes and gene expression changes in the central carbon metabolism for the analysis of 5 different perturbations. Out of 45 data points there were no more than 6 data points deviating from the correlation. Additionally, up- or down-regulation of at least 75% of the genes were in qualitative agreement with the CEF changes for all perturbations studied.

Conclusion
The analysis indicates that changes in carbon source are associated with a high degree of hierarchical regulation of metabolic fluxes in the central carbon metabolism as the change in fluxes are correlating directly with the change in transcript levels of genes encoding their corresponding enzymes. For amino acid biosynthesis there was, however, not found to exist a similar correlation, and this may point to either post-transcriptional and/or metabolic regulation, or be due to the absence of a direct perturbation on the amino acid pathways in these experiments.