Comparative assessment of radiation therapy-induced vasculitis using [18F]FDG-PET/CT in patients with non-small cell lung cancer treated with proton versus photon radiotherapy

PURPOSE

To assess radiation therapy (RT)-induced vasculitis in patients with non-small cell lung cancer (NSCLC) by examining changes in the uptake of 18F-fluoro-D-deoxyglucose ([18F]FDG) by positron emission tomography/computed tomography (PET/CT) images of the ascending aorta (AA), descending aorta (DA), and aortic arch (AoA) before and after proton and photon RT.

METHOD

Thirty-five consecutive locally advanced NSCLC patients were definitively treated with proton (n = 27) or photon (n = 8) RT and concurrent chemotherapy. The patients were prospectively enrolled to undergo [18F]FDG-PET/CT imaging before and 3 months after RT. An adaptive contrast-oriented thresholding algorithm was applied to generate mean standardized uptake values (SUVmean) for regions of interest (ROIs) 3 mm outside and 3 mm inside the outer perimeter of the AA, DA, and AoA. These ROIs were employed to exclusively select the aortic wall and remove the influence of blood pool activity. SUVmeans before and after RT were compared using two-tailed paired t-tests.

RESULTS

RT treatments were associated with increased SUVmeans in the AA, DA, and AoA-1.9%, 0.3%, and 1.3% for proton and 15.8%, 9.5%, and 15.5% for photon, respectively. There was a statistically significant difference in the ∆SUVmean (post-RT SUVmean - pre-RT SUVmean) in patients treated with photon RT when compared to ∆SUVmean in patients treated with proton RT in the AA (p = 0.043) and AoA (p = 0.015). There was an average increase in SUVmean that was related to dose for photon patients (across structures), but that was not seen for proton patients, although the increase was not statistically significant.

CONCLUSION

Our results suggest that patients treated with photon RT for NSCLC may exhibit significantly more RT-induced inflammation (measured as ∆SUVmean) in the AA and AoA when compared to patients who received proton RT. Knowledge gained from further analyses in larger cohorts could aid in treatment planning and help prevent the significant morbidity and mortality associated with RT-induced vascular complications.

TRIAL REGISTRATION

NCT02135679.

Discrepancies between tumor genomic profiling and germline genetic testing

BACKGROUND

Tumor genomic profiling (TGP) often incidentally identifies germline pathogenic variants (PVs) associated with cancer predisposition syndromes. Methods used by somatic testing laboratories, including germline analysis, differ from designated germline laboratories that have optimized the identification of germline PVs. This study evaluated discrepancies between somatic and germline testing results, and their impact on patients.

PATIENTS AND METHODS

Chart reviews were carried out at a single institution for patients who had both somatic and designated germline genetic testing. Cases with discrepant results in which germline PVs were not detected by the somatic laboratory or in which variant classification differed are summarized.

RESULTS

TGP was carried out on 2811 cancer patients, 600 of whom also underwent designated germline genetic testing. Germline PVs were identified for 109 individuals. Discrepancies between germline genetic testing and tumor profiling reports were identified in 20 cases, including 14 PVs identified by designated germline genetic testing laboratories that were not reported by somatic testing laboratories and six variants with discrepant classifications between the designated germline and somatic testing laboratories. Three PVs identified by designated germline laboratories are targets for poly adenosine diphosphate-ribose polymerase (PARP) inhibitors and resulted in different treatment options. Of the PVs identified by designated germline laboratories, 60% (n = 12) were in genes with established associations to the patients' cancer, and 40% of the PVs were incidental. The majority (90%) of all discrepant findings, both contributory and incidental, changed management recommendations for these patients, highlighting the importance of comprehensive germline assessment.

CONCLUSIONS

Methods used by somatic laboratories, regardless of the inclusion of germline analysis, differ from those of designated germline laboratories for identifying germline PVs. Unrecognized germline PVs may harm patients by missing hereditary syndromes and targeted therapy opportunities (e.g. anti-programmed cell death protein 1 immunotherapy, PARP inhibitors). Clinicians should refer patients who meet the criteria for genetic evaluation regardless of somatic testing outcomes.

Gas-loading furnace for deuterium-charged alloy-casting

A furnace was developed and characterized to allow for safe and controlled gas-loading or degassing of alloys. This oven is able to process samples under varying atmospheres, such as high vacuum or nitrogen containing 10 vol. % deuterium, as well as for pressures up to 800 hPa. Thermal desorption spectroscopy and scanning electron microscopy demonstrate the enhancing effects of high loading-gas concentration, high pressures, high temperatures above liquidus (50-150 K above the liquidus temperature of the cast hypoeutectic aluminum-copper model-alloy), and long holding times (up to 60 min) on the amount of retained gas in the solidified sample. Lack of copper segregation in the casting is confirmed by energy dispersive x-ray diffraction and Rutherford backscattering spectroscopy. It is shown that the facility allows for the controlled generation of distinct amounts of gas pores, down to a nil amount (only shrinkage porosity appearing in the sample).

[Use of near-infrared spectroscopy for control of limb perfusion during venoarterial ECMO treatment : Application and limitations]

Patients undergoing peripheral venoarterial extracorporeal membrane oxygenation have a high risk of lower limb ischemia. In general, regular controls are carried out based on clinical and laboratory parameters in order to quickly detect and treat complications. These controls are challenging due to states of shock, nonpulsatile flow and vasopressor therapy. As additional monitoring the use of near-infrared spectroscopy (NIRS) is described in the literature as being very successful in detecting ischemia. The present article describes the use and possible limitations of NIRS for the diagnostics of peripheral ischemia.

Towards clinical application: prompt gamma imaging of passively scattered proton fields with a knife-edge slit camera

Prompt γ-ray imaging with a knife-edge shaped slit camera provides the possibility of verifying proton beam range in tumor therapy. Dedicated experiments regarding the characterization of the camera system have been performed previously. Now, we aim at implementing the prototype into clinical application of monitoring patient treatments. Focused on this goal of translation into clinical operation, we systematically addressed remaining challenges and questions. We developed a robust energy calibration routine and corresponding quality assurance protocols. Furthermore, with dedicated experiments, we determined the positioning precision of the system to 1.1 mm (2σ). For the first time, we demonstrated the application of the slit camera, which was intentionally developed for pencil beam scanning, to double scattered proton beams. Systematic experiments with increasing complexity were performed. It was possible to visualize proton range shifts of 2-5 mm with the camera system in phantom experiments in passive scattered fields. Moreover, prompt γ-ray profiles for single iso-energy layers were acquired by synchronizing time resolved measurements to the rotation of the range modulator wheel of the treatment system. Thus, a mapping of the acquired profiles to different anatomical regions along the beam path is feasible and additional information on the source of potential range shifts can be obtained. With the work presented here, we show that an application of the slit camera in clinical treatments is possible and of potential benefit.

[Effects of Vibrax (Mechanical Vibrations) on the Arterial Blood Gases of Patients in the Intensive Care Unit after Cardiac Surgery]

OBJECTIVE

Respiratory physiotherapy is an integral part of the care of patients in intensive care units (ICU) after cardiac surgery. One of the most commonly used techniques in ICU to prevent pulmonary complications are mechanical vibrations, which can be applied with a tool called Vibrax.The aim of this study was to investigate the effects of Vibrax (mechanical vibrations) on the arterial blood gases of patients in ICU during the 1. or 2. day after cardiac surgery.

METHODS

A randomized controlled pilot study was conducted with 23 patients. The participants of the control group (CG) received a cardiovascular training with mobilization to the edge of the bed and active breathing exercises. On the patients of the intervention group (IG) additionally Vibrax was applied for 5 minutes. As primary outcome parameter the PaO2/FiO2 ratio was measured.

RESULTS

In the CG no significant changes over time were observed (p ≥ 0.06). The IG showed a significant (p = 0.009) increase in the PaO2/FiO2 ratio from before the physiotherapy intervention (M = 296.52, SE = 34.94 mmHg) to 60 minutes after completion of the physiotherapy intervention (M = 331.39, SE = 48.14 mmHg). There was no significant difference between the CG and IG at any measuring time (p ≥ 0.09).

CONCLUSION

The results of this pilot study indicate that the application of Vibrax has positive effects on the arterial blood gases of patients in ICU on the 1. or 2. day after cardiac surgery. But whether the effects are clinically relevant could not be clarified.

Atom economical synthesis of di- and trithiocarbonates by the lithium tert-butoxide catalyzed addition of carbon disulfide to epoxides and thiiranes

The lithium tert-butoxide catalyzed addition of CS₂ to epoxides and thiiranes under mild conditions is reported. A mechanism has been proposed taking into account the regio- and stereochemical outcome of the reaction.

Soil biota effects on local abundances of three grass species along a land-use gradient

Biotic plant-soil interactions and land-use intensity are known to affect plant individual fitness as well as competitiveness and therefore plant-species abundances in communities. Therefore, a link between soil biota and land-use intensity on local abundance of plant species in grasslands can be expected. In two greenhouse experiments, we investigated the effects of soil biota from grassland sites differing in land-use intensity on three grass species that vary in local abundances along this land-use gradient. We were interested in those soil-biota effects that are associated with land-use intensity, and whether these effects act directly or indirectly. Therefore, we grew the three plant species in two separate experiments as single individuals and in mixtures and compared their performance. As single plants, all three grasses showed a similar performance with and without soil biota. In contrast, in mixtures growth of the species in response to the presence or absence of soil biota differed. This resulted in different soil-biota effects that tend to correspond with patterns of species-specific abundances in the field for two of the three species tested. Our results highlight the importance of indirect interactions between plants and soil microorganisms and suggest that combined effects of soil biota and plant-plant interactions are involved in structuring plant communities. In conclusion, our experiments suggest that soil biota may have the potential to alter effects of plant-plant interactions and therefore influence plant-species abundances and diversity in grasslands.

[Improvement of cost allocation in gastroenterology by introduction of a novel service catalogue covering the complete spectrum of endoscopic procedures]

BACKGROUND

The German hospital reimbursement system (G-DRG) is incomplete for endoscopic interventions and fails to differentiate between complex and simple procedures. This is caused by outdated methods of personnel-cost allocation.

METHODS

To establish an up-to-date service catalogue 50 hospitals made their anonymized expense-budget data available to the German-Society-of-Gastroenterology (DGVS). 2.499.900 patient-datasets (2011-2013) were used to classify operation-and-procedure codes (OPS) into procedure-tiers (e.g. colonoscopy with biopsy/colonoscopy with stent-insertion). An expert panel ranked these tiers according to complexity and assigned estimates of physician time. From June to November 2014 exact time tracking data for a total 38.288 individual procedures were collected in 119 hospitals to validate this service catalogue.

RESULTS

In this three-step process a catalogue of 97 procedure-tiers was established that covers 99% of endoscopic interventions performed in German hospitals and assigned validated mean personnel-costs using gastroscopy as standard. Previously, diagnostic colonoscopy had a relative personnel-cost value of 1.13 (compared to gastroscopy 1.0) and rose to 2.16, whereas diagnostic ERCP increased from 1.7 to 3.62, more appropriately reflecting complexity. Complex procedures previously not catalogued were now included (e.g. gastric endoscopic submucosal dissection: 16.74).

DISCUSSION

This novel service catalogue for GI-endoscopy almost completely covers all endoscopic procedures performed in German hospitals and assigns relative personnel-cost values based on actual physician time logs. It is to be included in the national coding recommendation and should replace all prior inventories for cost distribution. The catalogue will contribute to a more objective cost allocation and hospital reimbursement - at least until time tracking for endoscopy becomes mandatory.

L1₀ FePtCu bit patterned media

Chemically ordered 5 nm-thick L1₀ FePtCu films with strong perpendicular magnetic anisotropy were post-patterned by nanoimprint lithography into a dot array over a 3 mm-wide circumferential band on a 3 inch Si wafer. The dots with a diameter of 30 nm and a center-to-center pitch of 60 nm appear as single domain and reveal an enhanced switching field as compared to the continuous film. We demonstrate successful recording on a single track using shingled writing with a conventional hard disk drive write/read head.

Elevated osteonectin/SPARC expression in primary prostate cancer predicts metastatic progression

BACKGROUND

The majority of prostate cancers (CaP) are detected in early stages with uncertain prognosis. Therefore, an intensive effort is underway to define early predictive markers of CaP with aggressive progression characteristics.

METHODS

In order to define such prognostic markers, we performed comparative analyses of transcriptomes of well- and poorly differentiated (PD) tumor cells from primary tumors of patients (N=40) with 78 months of mean follow-up after radical prostatectomy. Validation experiments were carried out at transcript level by quantitative real-time reverse transcriptase-PCR (RT-PCR) (N=110) and at protein level by immunohistochemistry (N=53) in primary tumors from an independent patient cohort.

RESULTS

Association of a biochemical network of 12 genes with SPARC gene as a central node was highlighted with PD phenotype. Of note, there was remarkable enrichment of NKXH_NKXH_HOX composite regulatory elements in the promoter of the genes in this network suggesting a biological significance of this gene-expression regulatory mechanism in CaP progression. Further, quantitative expression analyses of SPARC mRNA in primary prostate tumor cells of 110 patients validated the association of SPARC expression with poor differentiation and higher Gleason score. Most significantly, higher SPARC protein expression at the time of prostatectomy was associated with the subsequent development of metastasis (P=0.0006, AUC=0.803).

CONCLUSIONS

In summary, we propose that evaluation of SPARC in primary CaP has potential as a prognostic marker of metastatic progression.

Chemoproteomics-based kinome profiling and target deconvolution of clinical multi-kinase inhibitors in primary chronic lymphocytic leukemia cells

The pharmacological induction of apoptosis in neoplastic B cells presents a promising therapeutic avenue for the treatment of chronic lymphocytic leukemia (CLL). We profiled a panel of clinical multi-kinase inhibitors for their ability to induce apoptosis in primary CLL cells. Whereas inhibitors targeting a large number of receptor and intracellular tyrosine kinases including c-KIT, FLT3, BTK and SYK were comparatively inactive, the CDK inhibitors BMS-387032 and flavopiridol showed marked efficacy similar to staurosporine. Using the kinobeads proteomics method, kinase expression profiles and binding profiles of the inhibitors to target protein complexes were quantitatively monitored in CLL cells. The targets most potently affected were CDK9, cyclin T1, AFF3/4 and MLLT1, which may represent four subunits of a deregulated positive transcriptional elongation factor (p-TEFb) complex. Albeit with lower potency, both drugs also bound the basal transcription factor BTF2/TFIIH containing CDK7. Staurosporine and geldanamycin do not affect these targets and thus seem to exhibit a different mechanism of action. The data support a critical role of p-TEFb inhibitors in CLL that supports their future clinical development.

A Genomic Biomarker for Breast Cancer Development in High-Risk Women

BackgroundFamily history is an important factor contributing to a woman's risk of breast cancer development. This increased risk reflects the participation of inherited genetic components such as breast cancer susceptibility genes. However, many of the genetic components contributing to breast cancer remain unknown, and a number of women with a family history of breast cancer never develop breast cancer despite their high-risk status, while other high-risk woman go on to develop breast cancer. Thus, it is clear that we lack crucial pieces of information to help define a person's true risk of developing breast cancer.Methods and FindingsWe hypothesize that there are many undiscovered germline variations in genes that lead to altered gene expression patterns predictive of breast cancer development in high-risk women. We have developed a genomic model capable of predicting which high-risk women, both BRCA1/2 mutation carriers and BRCAX women, will actually develop breast cancer. Specifically, we use exon-level genome-wide expression profiling of peripheral blood mononuclear cells (PBMCs) to develop a model of disease risk (n=118 samples of either control or high-risk women). From this data, we generate a biomarker consisting of genes that most correlate to cancer development in women with strong family histories of breast cancer. Using an internal independent dataset, our biomarker can predict the high-risk women who will or will not develop cancer with over 85% accuracy. Further, we have validated this model on an independent external cohort (n=36) which was obtained and processed at sites unique to our training dataset. Our genomic biomarker can accurately predict breast cancer development in high-risk women with over 78% accuracy using this external dataset. Therefore, from our analyses, we can calculate with high accuracy an individual woman's true risk of developing breast cancer. This method provides a personalized approach to hereditary breast cancer risk assessment that is not currently available. This personalized risk assessment will aide clinicians in counseling their patients regarding specific management options based on a patient's individual risk of breast cancer. Lastly, these studies have also identified novel genes associated with breast cancer risk, which may provide a basis for targeted therapies that may help modify the risk of breast cancer development in high risk patients.ConclusionsTogether, these studies deliver both a non-invasive biomarker for hereditary breast cancer risk and a characterization of genes that contribute to breast cancer development. Overall, we expect these experiments to identify the genetic changes that underlie breast cancer predisposition, and assist clinicians and patients in determining the appropriate preventative measures based on their personal risk of developing breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4059.

Transcriptome analyses of benign and malignant prostate epithelial cells in formalin-fixed paraffin-embedded whole-mounted radical prostatectomy specimens

Formalin-fixed paraffin-embedded (FFPE) prostate specimens are rich sources of molecular pathological information. However, FFPE-based microarray analysis of tissue samples may be hampered by the degradation and chemical alteration of RNA molecules due to the preservation procedure. In this report, we employed a probe analyses of Affymetrix oligonucleotide arrays at individual probe level to compensate for the potential loss of gene identifications associated with compromised mRNA quality in FFPE preparations. Furthermore, to increase the sample quality, we utilized laser capture microdissection of prostate tumor and benign epithelial cells. Remarkably, combination of these approaches recapitulated the common prostate cancer-associated gene expression alteration. Identification of prostate cancer associated-gene expression alterations such as AMACR, Kallikrein gene family and genes associated with androgen signaling such as PDEF and STEAP were consistent with previous findings reported in prostate cancer. These data suggest that combination of laser capture dissection with computational enhancement of microarray data may be useful for the assessment of gene expression changes in FFPE prostate cancer specimens.

Efforts to establish an animal model of Fanconi syndrome after ifosfamide administration to rats

About 10% of children develop Fanconi syndrome (FS) a few months after ifosfamide (IFO) treatment. To establish an animal model, IFO was injected as 4 or 5 treatment courses (TCs, once daily for 3 consecutive days), to adult female rats (AF, 8 mg 100 g(-1) body wt, 4 TCs), to young female rats (YF, 8 mg 100 g(-1) body wt, 5 TCs) and to male rats (M, 6 mg 100 g(-1) body wt, 4 TCs). In the adult female rats, polyuria with electrolyte and albumin wasting occurred acutely, 2 days after the first treatment course. After the third treatment course, 30% of the rats died, but survivors showed a reduced excretion of electrolytes and glucose. The body weight increase was significantly diminished in adult female and male rats by about 25% or 70%, respectively. Up to 5 months after 5 TCs in young female rats, 15% of the animals died but the survivors did not show any sign of renal failure. In males, 28% of the rats died and in surviving animals the excretion of electrolytes, proteins and glucose as well as GFR were reduced 7 weeks after the last treatment course. There were no pathomorphological changes in kidney and liver. Determination of renal and hepatic cytochrome P450 activities indicated that results of adult female and male rats could be caused by starving, known as a common side effect of IFO, and not by its nephrotoxicity. Altogether, it was not possible to establish a model of a Fanconi syndrome persisting after cessation of IFO treatment in our rat strain, whereas acute, FS-like IFO effects on the kidney could be shown.

The satiety factor apolipoprotein A-IV modulates intestinal epithelial permeability through its interaction with alpha-catenin: implications for inflammatory bowel diseases

INTRODUCTION

Apolipoprotein A-IV (apoA-IV), an intestinally and cerebrally synthesized satiety factor and anti-atherogenic plasma apolipoprotein, was recently identified as an anti-inflammatory protein. In order to elucidate whether intestinal apoA-IV exerts similar repair function as its hepatic homologue apolipoprotein A-V (apoA-V), apoA-IV-interactive proteins were searched and in vitro functional studies were performed with apoA-IV overexpressing cells. ApoA-IV was also analyzed in the intestinal mucosa of patients with inflammatory bowel diseases (IBD), together with other genes involved in epithelial junctional integrity.

METHODS

A yeast-two-hybrid screening was used to identify apoA-IV-interactors. ApoA-IV was overexpressed in Caco-2 and HT-29 mucosal cells for colocalization and in vitro epithelial permeability studies. Mucosal biopsies from quiescent regions of colon transversum and terminal ileum were subjected to DNA-microarray analysis and pathway-related data mining.

RESULTS

Four proteins interacting with apoA-IV were identified, including apolipoprotein B-100, alpha1-antichymotrypsin, cyclin C, and the cytosolic adaptor alpha-catenin, thus linking apoA-IV to adherens junctions. Overexpression of apoA-IV was paralleled with a differentiated phenotype of intestinal epithelial cells, upregulation of junctional proteins, and decreased paracellular permeability. Colocalization between alpha-catenin and apoA-IV occurred exclusively in junctional complexes. ApoA-IV was downregulated in quiescent mucosal tissues from patients suffering from IBD. In parallel, only a distinct set of junctional genes was dysregulated in non-inflamed regions of IBD gut.

CONCLUSIONS

ApoA-IV may act as a stabilizer of adherens junctions interacting with alpha-catenin, and is likely involved in the maintenance of junctional integrity. ApoA-IV expression is significantly impaired in IBD mucosa, even in non-inflamed regions.

The relationship between tumor size and stage in early versus advanced ovarian cancer: A retrospective chart review

5580

Background: Ovarian cancer has a different prognosis between early (I and II) and advanced stage (III and IV). The mechanism of disease progression is unknown, but patients with advanced disease may have a higher propensity for seeding of the abdominal cavity early in the disease process than those with early stage. Theoretically if this is so, then patients with advanced stage should have smaller sized tumors than patients with early stage. Methods: This was a retrospective chart review of patients in the tumor registry in 2003 to 2006. Patients had epithelial ovarian cancer, other cell types were excluded. Only cases with documentation of surgical and pathologic staging and measured dimensions on pathologic specimen were included. Patient stage and all available dimensions measured on diseased ovaries were recorded. The dimensions for each patient were averaged into a single dimension for that patient, and then these measurements were totaled and averaged. Results: There were 110 patients analyzed: 85 with advanced disease, 25 with early stage. The average measurement was 4.8 cm in advanced disease, and was 10.7 cm in early stage disease. This difference was statistically significant (p < 0.001). Conclusions: Overall, patients with early stage ovarian cancer have diseased ovaries that are more than twice as large as those found in advanced disease. This finding supports the fact that early versus advanced ovarian cancer are 2 separate disease processes. Early stage grows locally and does not disseminate, and advanced stage disseminates while the tumor is still relatively small. Theoretically there may be a factor that separates these 2 into different diseases, where advanced disease patients have a substance produced by their tumor that allows for early dissemination, and early stage lacks this substance and only grows locally. Basic science research comparing the tissue microarrays of early versus advanced stage disease may be able to identify this difference. If the difference is found, perhaps therapy can be targeted against this difference.

No significant financial relationships to disclose.

New insights into the biology of cytokinin degradation

A survey of recent results is presented concerning the role of cytokinin degradation in plants, which is catalyzed by cytokinin oxidase/dehydrogenase (CKX) enzymes. An overview of Arabidopsis CKX gene expression suggests that their differential regulation by biotic and abiotic factors contributes significantly to functional specification. Here, we show using reporter gene and semiquantitative RT-PCR analyses regulation of individual CKX genes by cytokinin, auxin, ABA, and phosphate starvation. Partially overlapping expression domains of CKX genes and cytokinin-synthesizing IPT genes in meristematic tissues and endo-reduplicating cells lend support for a locally restricted function of cytokinin. On the other hand, their expression in vascular tissue suggests a function in controlling transported cytokinin. Recent studies led to a model for the biochemical reaction mechanism of CKX-mediated catalysis, which was refined on the basis of the three-dimensional enzyme structure. Last but not least, the developmental functions of CKX enzymes are addressed. The recent identification of the rice OSCKX2 gene as an important novel breeding tool is highlighted. Together the results corroborate the relevance of metabolic control in determining cytokinin activity.

MatInspector and beyond: promoter analysis based on transcription factor binding sites

MOTIVATION

Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes.

RESULTS

We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).

Linking disease-associated genes to regulatory networks via promoter organization

Pathway- or disease-associated genes may participate in more than one transcriptional co-regulation network. Such gene groups can be readily obtained by literature analysis or by high-throughput techniques such as microarrays or protein-interaction mapping. We developed a strategy that defines regulatory networks by in silico promoter analysis, finding potentially co-regulated subgroups without a priori knowledge. Pairs of transcription factor binding sites conserved in orthologous genes (vertically) as well as in promoter sequences of co-regulated genes (horizontally) were used as seeds for the development of promoter models representing potential co-regulation. This approach was applied to a Maturity Onset Diabetes of the Young (MODY)-associated gene list, which yielded two models connecting functionally interacting genes within MODY-related insulin/glucose signaling pathways. Additional genes functionally connected to our initial gene list were identified by database searches with these promoter models. Thus, data-driven in silico promoter analysis allowed integrating molecular mechanisms with biological functions of the cell.

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources

SUMMARY

The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided.

AVAILABILITY

The HNB portal is available at http://www.hnbioinfo.de

Epidemiologie und Therapie der Lyme-Arthritis und anderer Manifestationen der Lyme-Borreliose in Deutschland

AIM OF THE STUDY

Only little is known about the epidemiology of Lyme borreliosis in Germany. As an example, it is still unclear if there are regional differences in the incidence of Lyme disease in general or of certain clinical manifestations like Lyme arthritis. Moreover, standardization of diagnostic or therapeutic procedures does not exist. Therefore, a Germany-wide questionnaire-based survey was conducted in order to achieve more epidemiological data and to obtain more information about the diagnostic and therapeutic approaches of general practitioners and specialists.

METHODS

A self-designed questionnaire was distributed along with two editions of the journal "Deutsches Arzteblatt" (which is delivered to every physician in Germany) and additionally by a pharmaceutical company. During the collection period from March 1, 1998 to February 28, 1999, patients with Lyme disease were reported and information was given about site of infection, diagnostic procedures, clinical symptoms, treatment, and outcome.

RESULTS

Altogether 3935 patients were reported. Their mean age was 43.4 years with the peak incidences around the ages of 10 and 60 years. 37.3% of the questionnaires were sent in by general practitioners, 17.6% by dermatologists, 15.7% by pediatricians, 9.7% by internists, and 2.7% by neurologists. 83% of the patients did not have a special infecion risk. The most frequent clinical Lyme manifestation was erythema migrans (EM), which occurred in 50.9% of the patients. 21.3% suffered from general symptoms. Of special interest, 24.5% of the patients had Lyme arthritis (14.7% mon- or oligoarthritis, 9.8% polyarthritis). Therefore, arthritis was more frequently reported than neuroborreliosis (18.4%). Only 16% of the neuroborreliosis patients and 32% of the arthritis patients remembered having had an EM. 189 patients (4.8%) with lymphadenosis cutis benigna and 100 patients (2.5%) with acrodermatitis chronica atrophicans were reported. In 80.4% of the patients, positive Lyme serology was detected. In a few cases, the diagnosis was established by isolation of borreliae, PCR or histology. 3754 patients were treated by antibiotics. The most frequently used compounds were doxycycline (50.4%), followed by ceftriaxone (22.4%), amoxicillin (13.6%), penicillin (7%), and erythromycin (4.2%) with differences depending on clinical manifestations and specialization of the prescribing physician. In less than 10% of the cases, not evaluated or recommended therapeutic procedures were performed.

DISCUSSION

Lyme disease is endemic throughuot Germany. The most frequent manifestations are EM, followed by Lyme arthritis and neuroborreliosis. Less than one third of patients suffering from disseminated or chronic Lyme disease remembered an EM. Most of the physicians taking part in this survey follow treatment recommendations concerning choice of antibiotics and treatment durations.

[Teleteaching in otorhinolaryngology. Part 2: the European database "medicstream"]

Searching the medical literature is mainly characterized by the use of databases. The time for reviewing and printing a paper causes a delay between the first presentation of scientific results in a lecture and the appearance of the appropriate journal publication. Moreover, the possibilities for the integration of multimedia data are limited. Because of the development of new compression algorithms for audiovisual digitization software, the near simultaneous transmission of scientific presentations, both visually and aurally, has been possible since 1999. The section telemedicine of the interdisciplinary study group on image guided surgical navigation from the University of Leipzig has developed "medicstream" as a unique, audiovisual, scientific internetdatabase. It allows the documentation of presentations at congresses and courses, including the discussion,over a freely accessible, widely available homepage, using a home developed streaming technology. All presentations are examined by an authorized editorial committee consisting of representatives with different medical specializations for content before the admission to the data base. A total of 392 presentations from seven scientific meetings can be selected by an integrated search machine and viewed with Windows Media Player or Real Player using a conventional or faster internet connection to the homepage www.medicstream.de. The quality of the audiovisual transmission depends on the receiver-lateral data transmission rate,whereby the minimum variant of 56 kB/s is characterized by good detectability of the contents. In an analysis period of 242 days,we registered 44,199 accesses and 4,488 attendances. The telemedicine data base "medicstream" can optimize quality and extend medical education by live-streaming as well as by archiving scientific presentations as audiovisual data.

[Teleteaching in otorhinolaryngology (part 1). Real-time transmission of a congress in picture and tone into the Internet]

The transmission of scientific seminars into the Internet represents a new application of modern technologies for teleteaching. We digitally recorded 74 seminars and discussions during the 8th annual meeting of the German Society of Skull Base Surgery with five cameras and eight microphones, and transformed the data live with the real-Producer using a video card.This transferred data stream was sent via ISDN (128 kbit/s) to a real-server at the university, which was used for distribution in the net. The seminars could be called up in the display format of 320x240 pixels with a delay of 3 min (minimum: 30 s, as a function of the connection of the user) at each computer with Internet entrance. Altogether,we registered 3,284 accesses to the presentations following the congress until June 2002. The quality of picture transmission (24-36 kbit/s) and the quality of tone (audio stream: 5 kbit/s) were sufficient to understand the contents of the slide, video or computer presentation. The transmission of scientific meetings into the Internet can increase, with a justifiable technical expenditure, their efficiency by the ubiquitous availability of the information and the extension of the audience.

Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach

Transcriptional regulation depends on the binding of transcription factors to their corresponding binding sites. The response to cellular signals is often mediated by the cooperative binding of transcription factors to well defined regulatory modules consisting of at least two transcription factor binding sites. Such regulatory modules can be responsible for the common regulation of genes within a gene class or confer a common function to promoters belonging to different gene classes. We developed in silico models representing a common framework of potential regulatory sites specific for one promoter class (actins). We also generated models for two different functional promoter modules both of which confer responsiveness to tumor necrosis factor (TNF) and interferon (IFN) to a variety of promoters. All models exhibited high selectivity, e.g. the mammalian muscle actin promoter model produced no false negatives in a database search.