Copasetic analysis: a framework for the blind analysis of microarray imagery

The official published version can be found at the link below.From its conception, bioinformatics has been a multidisciplinary field which blends domain expert knowledge with new and existing processing techniques, all of which are focused on a common goal. Typically, these techniques have focused on the direct analysis of raw microarray image data. Unfortunately, this fails to utilise the image's full potential and in practice, this results in the lab technician having to guide the analysis algorithms. This paper presents a dynamic framework that aims to automate the process of microarray image analysis using a variety of techniques. An overview of the entire framework process is presented, the robustness of which is challenged throughout with a selection of real examples containing varying degrees of noise. The results show the potential of the proposed framework in its ability to determine slide layout accurately and perform analysis without prior structural knowledge. The algorithm achieves approximately, a 1 to 3 dB improved peak signal-to-noise ratio compared to conventional processing techniques like those implemented in GenePix® when used by a trained operator. As far as the authors are aware, this is the first time such a comprehensive framework concept has been directly applied to the area of microarray image analysis

Hybrid clustering for microarray image analysis combining intensity and shape features

BACKGROUND: Image analysis is the first crucial step to obtain reliable results from microarray experiments. First, areas in the image belonging to single spots have to be identified. Then, those target areas have to be partitioned into foreground and background. Finally, two scalar values for the intensities have to be extracted. These goals have been tackled either by spot shape methods or intensity histogram methods, but it would be desirable to have hybrid algorithms which combine the advantages of both approaches. RESULTS: A new robust and adaptive histogram type method is pixel clustering, which has been successfully applied for detecting and quantifying microarray spots. This paper demonstrates how the spot shape can be effectively integrated in this approach. Based on the clustering results, a bivalence mask is constructed. It estimates the expected spot shape and is used to filter the data, improving the results of the cluster algorithm. The quality measure 'stability' is defined and evaluated on a real data set. The improved clustering method is compared with the established Spot software on a data set with replicates. CONCLUSION: The new method presents a successful hybrid microarray image analysis solution. It incorporates both shape and histogram features and is specifically adapted to deal with typical microarray image characteristics. As a consequence of the filtering step pixels are divided into three groups, namely foreground, background and deletions. This allows a separate treatment of artifacts and their elimination from the further analysis

Motor-evoked potentials (MEP) during brainstem surgery to preserve corticospinal function

Background: Brainstem surgery bears a risk of damage to the corticospinal tract (CST). Motor-evoked potentials (MEPs) are used intraoperatively to monitor CST function in order to detect CST damage at a reversible stage and thus impede permanent neurological deficits. While the method of MEP is generally accepted, warning criteria in the context of brainstem surgery still have to be agreed on. Method: We analyzed 104 consecutive patients who underwent microsurgical resection of lesions affecting the brainstem. Motor grade was documented prior to surgery, early postoperatively and at discharge. A baseline MEP stimulation intensity threshold was defined and intraoperative testing aimed to keep MEP response amplitude constant. MEPs were considered deteriorated and the surgical team was notified whenever the threshold was elevated by ≥20mA or MEP response fell under 50%. Findings: On the first postoperative day, 18 patients experienced new paresis that resolved by discharge in 11. MEPs deteriorated in 39 patients, and 16 of these showed new postoperative paresis, indicating a 41% risk of new paresis. In the remaining 2/18 patients, intraoperative MEPs were stable, although new paresis appeared postoperatively. In one of these patients, intraoperative hemorrhage caused postoperative swelling, and the new motor deficit persisted until discharge. Of all 104 patients, 7 deteriorated in motor grade at discharge, 92 remained unchanged, and 5 patients have improved. Conclusions: Adjustment of surgical strategy contributed to good motor outcome in 33/39 patients. MEP monitoring may help significantly to prevent motor deficits during demanding neurosurgical procedures on the brainste

Surgical treatment of tentorial dural arteriovenous fistulae located around the tentorial incisura

Tentorial dural arteriovenous fistulae (DAVF) are relatively uncommon and are the most dangerous type of DAVF. Because of a high incidence of hemorrhage and subsequent neurological deficits, treatment is mandatory. A consecutive series of nine surgically treated patients with symptomatic tentorial DAVF were analyzed in this study. All lesions were located around the tentorial incisura and were treated microsurgically using a subtemporal approach in eight cases and a supracerebellar approach in one case. The dural bases of the lesions were located adjacent to the tentorial edge in six patients and the tentorial apex in three patients. Complete obliteration was achieved in all treated tentorial DAVF. In one patient, the torcular fistula remained untreated without cortical venous reflux. Postoperative asymptomatic temporal lobe hemorrhage was diagnosed in one patient with a tentorial apex DAVF; however, no new neurological symptoms were present after surgical treatment. The subtemporal approach for unilateral tentorial DAVF is a favorable and direct approach for the highly skilled surgeon. Perimesencephalic venous dilatation or varix is an important finding on MRI to help localize tentorial DAVF in the tentorial edge or ape

Surgical resection of pediatric skull base meningiomas

Purpose: Meningiomas in children are rare, especially those located at the skull base. In this study, we report our experience of meningioma surgery in the pediatric population and compare our findings of skull base (SB) versus non-skull base (NSB) meningiomas. Methods: From our database of 724 surgically treated meningioma patients at the University Hospital, Zurich between 1995 and 2010, 12 patients under 18years of age were identified. Data for those patients was retrospectively collected through chart review. A descriptive comparison between SB and NSB meningiomas was undertaken to determine statistical significance. Results: In all 12 children (seven males, five females; mean age 12.2 ± 4.3years), surgical removal of the meningioma was performed microsurgically with a mean follow-up of 53months (range 12-137months). Of the 12 tumors, six were located in the SB and six in the NSB. Comparing SB to NSB lesions, the mean age was 11 ± 3.8 versus 14 ± 4.6years, male/female gender distribution was 5:1 compared to 1:5, mean tumor size was 7.5 ± 6.2 versus 26 ± 15.8cm2 (p = 0.03), and mean surgery time was 347 versus 214min. While WHO grade was similar for both groups, the Simpson grade revealed more extensive resection for NSB meningiomas. The Glasgow Outcome Scale at last follow-up was favorable for both groups. Conclusions: Meningioma surgery was safe with favorable outcomes. SB meningiomas were significantly smaller in size, were less likely to undergo complete resection, and had a predilection for younger, male patient

Intraoperative low-field MR-guided frameless stereotactic biopsy for intracerebral lesions

Background: To present our intraoperative low-field magnetic resonance imaging (ioMRI) technique for stereotactic brain biopsy in various intracerebral lesions. Method: Seventy-eight consecutive patients underwent stereotactic biopsies with the PoleStar N-20/N-30 ioMRI system and data were evaluated retrospectively. Biopsy technique included ioMRI before surgery, followed by insertion of the biopsy cannula in the lesion, and ioMRI before and after biopsy. Statistical analysis was performed to compare subgroups using Excel and SPSS statistic software. Results: In all patients, stereotactic biopsy was possible, with a mean intraoperative surgery time of 86.2 ± 28.6min and a mean hospital stay of 11.6 ± 4.6days. In 97.4% (n = 76), histology was conclusive, representing 58 brain tumors and 18 other pathologies. Five patients were biopsied previously without conclusive diagnosis, and all biopsies were conclusive this time. Mean cross-sectional lesion size in MRI T1 with contrast (n = 64) was 6.9 ± 5.7cm2, and in lesions without T1 contrast enhancement (n = 14), T2 mean cross-sectional lesion size was 5.5 ± 3.9cm2. Mean distance from the cortex surface to the lesion was 3.4 ± 1.2cm. One patient suffered from a postoperative wound dehiscence; neither clinically or radiologically significant hemorrhage after surgery, nor intraoperative complications occurred. Conclusions: Low-field ioMR-guided frameless stereotactic biopsy accurately diagnosed different intracerebral lesions without major complications for the patients, and within an acceptable surgery time and hospital stay. In repeated non-conclusive biopsies in particular, low-field ioMRI offers a technique for arriving at a diagnosi

Resection of pediatric intracerebral tumors with the aid of intraoperative real-time 3-D ultrasound

Purpose: Intraoperative ultrasound (IOUS) has become a useful tool employed daily in neurosurgical procedures. In pediatric patients, IOUS offers a radiation-free and safe imaging method. This study aimed to evaluate the use of a new real-time 3-D IOUS technique (RT-3-D IOUS) in our pediatric patient cohort. Material and methods: Over 24months, RT-3-D IOUS was performed in 22 pediatric patients (8 girls and 14 boys) with various brain tumors. These lesions were localized by a standard navigation system followed by analyses before, intermittently during, and after neurosurgical resection using the iU22 ultrasound system (Philips, Bothell, USA) connected to the RT-3-D probe (X7-2). Results: In all 22 patients, real-time 3-D ultrasound images of the lesions could be obtained during neurosurgical resection. Based on this imaging method, rapid orientation in the surgical field and the approach for the resection could be planned for all patients. In 18 patients (82%), RT-3-D IOUS revealed a gross total resection with a favorable neurological outcome. Conclusion: RT-3-D IOUS provides the surgeon with advanced orientation at the tumor site via immediate live two-plane imaging. However, navigation systems have yet to be combined with RT-3-D IOUS. This combination would further improve intraoperative localizatio

Intra-operative high frequency ultrasound improves surgery of intramedullary cavernous malformations

Intra-operative ultrasound (ioUS) is a very useful tool in surgery of spinal lesions. Here we focus on modern ioUS to analyze its use for localisation, visualisation and resection control in intramedullary cavernous malformations (IMCM). A series of 35 consecutive intradural lesions were operated in our hospital in a time period of 24months using modern ioUS with a high frequency 7-15MHz transducer and a true real time 3D transducer (both Phillips iU 22 ultrasound system). Six of those cases were treated with the admitting diagnosis of a deep IMCM (two cervical, four thoracic lesions). IoUS images were performed before and after the IMCM resection. Pre-operative and early postoperative MRI images were performed in all patients. In all six IMCM cases a complete removal of the lesion was achieved microsurgically resulting in an improved neurological status of all patients. High frequency ioUS emerged to be a very useful tool during surgery for localization and visualization. Excellent resection control by ultrasound was possible in three cases. Minor resolution of true real time 3D ioUS decreases the actual advantage of simultaneous reconstruction in two planes. High frequency ioUS is the best choice for intra-operative imaging in deep IMCM to localize and to visualize the lesion and to plan the perfect surgical approach. Additionally, high frequency ioUS is suitable for intra-operative resection control of the lesion in selected IMCM case

Neurosurgical education in Europe and the United States of America

Training in neurological surgery is one of the most competitive and demanding specializations in medicine. It therefore demands careful planning in both the scientific and clinical neurosurgery arena to finally turn out physicians that can be clinically sound and scientifically competitive. National and international training and career options are pointed out, based on the available relevant literature, with the objective of comparing the neurosurgical training in Europe and the USA. Despite clear European Association of Neurosurgical Societies guidelines, every country in Europe maintains its own board requirements, which is reflected in an institutional curriculum that is specific to the professional society of that particular country. In contrast, the residency program in the USA is required to comply with the Accreditation Council for Graduate Medical Education guidelines. Rather similar guidelines exist for the education of neurosurgical residents in the USA and Europe; their translation into the practical hospital setting and the resulting clinical lifestyle of a resident diverges enormously. Since neurosurgical education remains heterogeneous worldwide, we argue that a more standardized curriculum across different nations would greatly facilitate the interaction of different centers, allow a direct comparison of available services, and support the exchange of vital information for quality control and future improvements. Furthermore, the exchange of residents between different training centers may improve education by increasing their knowledge base, both technically as well as intellectuall