Safety of elective paediatric surgery during the coronavirus disease 2019 pandemic.

INTRODUCTION: Corona-virus Disease 2019 (COVID-19) has had a huge impact on the delivery of healthcare worldwide, particularly elective surgery. There is a lack of data regarding risk of postoperative COVID-19 infection in children undergoing elective surgery, and regarding the utility of pre-operative COVID-19 testing, and preoperative "cocooning" or restriction of movements. The purpose of this present study was to examine the safety of elective paediatric Otolaryngology surgery during the COVID-19 pandemic with respect to incidence of postoperative symptomatic COVID-19 infection or major respiratory complications. MATERIALS AND METHODS: Prospective cohort study of paediatric patients undergoing elective Otolaryngology surgery between September and December 2020. Primary outcome measure was incidence of symptomatic COVID-19 or major respiratory complications within the 14 days after surgery. Parents of prospectively enrolled patients were contacted 14 days after surgery and enquiry made regarding development of postoperative symptoms, COVID-19 testing, or diagnosis of COVID-19. RESULTS: 302 patients were recruited. 125 (41.4%) underwent preoperative COVID-19 RT-PCR testing. 66 (21.8%) restricted movements prior to surgery. The peak 14-day COVID-19 incidence during the study was 302.9 cases per 100,000 population. No COVID-19 infections or major respiratory complications were reported in the 14 day follow-up period. CONCLUSION: The results of our study support the safety of elective paediatric Otolaryngology surgery during the pandemic, in the setting of community incidence not exceeding that observed during the study period.

Risk of disease transmission from flexible nasoendoscopy during the coronavirus disease 2019 pandemic.

BACKGROUND: Concerns have emerged regarding infection transmission during flexible nasoendoscopy. METHODS: Information was gathered prospectively on flexible nasoendoscopy procedures performed between March and June 2020. Patients and healthcare workers were followed up to assess for coronavirus disease 2019 development. One-sided 97.5 per cent Poisson confidence intervals were calculated for upper limits of risk where zero events were observed. RESULTS: A total of 286 patients were recruited. The most common indication for flexible nasoendoscopy was investigation of 'red flag' symptoms (67 per cent). Forty-seven patients (16 per cent, 95 per cent confidence interval = 13-21 per cent) had suspicious findings on flexible nasoendoscopy requiring further investigation. Twenty patients (7.1 per cent, 95 per cent confidence interval = 4.4-11 per cent) had new cancer diagnoses. Zero coronavirus disease 2019 infections were recorded in the 273 patients. No. 27 endoscopists (the doctors and nurses who carried out the procedures) were followed up.The risk of developing coronavirus disease 2019 after flexible nasoendoscopy was determined to be 0-1.3 per cent. CONCLUSION: The risk of coronavirus disease 2019 transmission associated with performing flexible nasoendoscopy in asymptomatic patients, while using appropriate personal protective equipment, is very low. Additional data are required to confirm these findings in the setting of further disease surges.

Three-dimensional Monte Carlo-based voxel-wise tumor dosimetry in patients with neuroendocrine tumors who underwent 177Lu-DOTATOC therapy.

BACKGROUND: Patients with advanced neuroendocrine tumors (NETs) of the midgut are suitable candidates for 177Lu-DOTATOC therapy. Integrated SPECT/CT systems have the potential to help improve the accuracy of patient-specific tumor dosimetry. Dose estimations to target organs are generally performed using the Medical Internal Radiation Dose scheme. We present a novel Monte Carlo-based voxel-wise dosimetry approach to determine organ- and tumor-specific total tumor doses (TTD). METHODS: A cohort of 14 patients with histologically confirmed metastasized NETs of the midgut (11 men, 3 women, 62.3 ± 11.0 years of age) underwent a total of 39 cycles of 177Lu-DOTATOC therapy (mean 2.8 cycles, SD ± 1 cycle). After the first cycle of therapy, regions of interest were defined manually on the SPECT/CT images for the kidneys, the spleen, and all 198 tracer-positive tumor lesions in the field of view. Four SPECT images, taken at 4 h, 24 h, 48 h and 72 h after injection of the radiopharmaceutical, were used to determine their effective half-lives in the structures of interest. The absorbed doses were calculated by a three-dimensional dosimetry method based on Monte Carlo simulations. TTD was calculated as the sum of all products of single tumor doses with single tumor volumes divided by the sum of all tumor volumes. RESULTS: The average dose values per cycle were 3.41 ± 1.28 Gy (1.91-6.22 Gy) for the kidneys, 4.40 ± 2.90 Gy (1.14-11.22 Gy) for the spleen, and 9.70 ± 8.96 Gy (1.47-39.49 Gy) for all 177Lu-DOTATOC-positive tumor lesions. Low- and intermediate-grade tumors (G 1-2) absorbed a higher TTD compared to high-grade tumors (G 3) (signed-rank test, p = < 0.05). The pre-therapeutic chromogranin A (CgA) value and the TTD correlated significantly (Pearson correlation: = 0.67, p = 0.01). Higher TTD resulted in a significant decrease of CgA after therapy. CONCLUSION: These results suggest that Monte Carlo-based voxel-wise dosimetry is a very promising tool for predicting the absorbed TTD based on histological and clinical parameters.

A deep learning approach to radiation dose estimation.

Currently methods for predicting absorbed dose after administering a radiopharmaceutical are rather crude in daily clinical practice. Most importantly, individual tissue density distributions as well as local variations of the concentration of the radiopharmaceutical are commonly neglected. The current study proposes machine learning techniques like Green's function-based empirical mode decomposition and deep learning methods on U-net architectures in conjunction with soft tissue kernel Monte Carlo (MC) simulations to overcome current limitations in precision and reliability of dose estimations for clinical dosimetric applications. We present a hybrid method (DNN-EMD) based on deep neural networks (DNN) in combination with empirical mode decomposition (EMD) techniques. The algorithm receives x-ray computed tomography (CT) tissue density maps and dose maps, estimated according to the MIRD protocol, i.e. employing whole organ S-values and related time-integrated activities (TIAs), and from measured SPECT distributions of 177Lu radionuclei, and learns to predict individual absorbed dose distributions. In a second step, density maps are replaced by their intrinsic modes as deduced from an EMD analysis. The system is trained using individual full MC simulation results as reference. Data from a patient cohort of 26 subjects are reported in this study. The proposed methods were validated employing a leave-one-out cross-validation technique. Deviations of estimated dose from corresponding MC results corroborate a superior performance of the newly proposed hybrid DNN-EMD method compared to its related MIRD DVK dose calculation. Not only are the mean deviations much smaller with the new method, but also the related variances are much reduced. If intrinsic modes of the tissue density maps are input to the algorithm, variances become even further reduced though the mean deviations are less affected. The newly proposed hybrid DNN-EMD method for individualized radiation dose prediction outperforms the MIRD DVK dose calculation method. It is fast enough to be of use in daily clinical practice.

A comparison of methods for adapting [Formula: see text] dose-voxel-kernels to tissue inhomogeneities.

In [Formula: see text] radionuclide therapies, dosimetry is used for determining patient-individual dose burden. Standard approaches provide whole organ doses only. For assessing dose heterogeneity inside organs, voxel-wise dosimetry based on 3D SPECT/CT imaging could be applied. Often, this is achieved by convolving voxel-wise time-activity-curves with appropriate dose-voxel-kernels (DVK). The DVKs are meant to model dose deposition, and can be more accurate if modelled for the specific tissue type under consideration. In literature, DVKs are often not adapted to these inhomogeneities, or simple approximation schemes are applied. For 26 patients, which had previously undergone a [Formula: see text] -PSMA or -DOTATOC therapy, decay maps, mass-density maps as well as tissue-type maps were derived from SPECT/CT acquisitions. These were used for a voxel-based dosimetry based on convolution with DVKs (each of size [Formula: see text]) obtained by four different DVK methods proposed in literature. The simplest only considers a spatially constant soft-tissue DVK (herein named 'constant'), while others either take into account only the local density of the center voxel of the DVK (herein named 'center-voxel') or scale each voxel linearly according to the proper mass density deduced from the CT image (herein named 'density') or considered both the local mass density as well as the direct path between the center voxel and any voxel in its surrounding (herein named 'percentage'). Deviations between resulting dose values and those from full Monte-Carlo simulations (MC simulations) were compared for selected organs and tissue-types. For each DVK method, inter-patient variability was considerable showing both under- and over-estimation of energy dose compared to the MC result for all tissue densities higher than soft tissue. In kidneys and spleen, 'constant' and 'density'-scaled DVKs achieved estimated doses with smallest deviations to the full MC gold standard (∼[Formula: see text] underestimation). For low and high density tissue types such as lung and adipose or bone tissue, alternative DVK methods like 'center-voxel'- and 'percentage'- scaled achieved superior results, respectively. Concerning computational load, dose estimation with the DVK method 'constant' needs about 1.1 s per patient, center-voxel scaling amounts to 1.2 s, density scaling needs 1.4 s while percentage scaling consumes 860.3 s per patient. In this study encompassing a large patient cohort and four different DVK estimation methods, no single DVK-adaption method was consistently better than any other in case of soft tissue kernels. Hence in such cases the simplest DVK method, labeled 'constant', suffices. In case of tumors, often located in tissues of low (lung) or high (bone) density, more sophisticated DVK methods excel. The high inter-patient variability indicates that for evaluating new algorithms, a sufficiently large patient cohort needs to be involved.

Factors affecting accuracy of S values and determination of time-integrated activity in clinical Lu-177 dosimetry.

INTRODUCTION: In any radiotherapy, the absorbed dose needs to be estimated based on two factors, the time-integrated activity of the administered radiopharmaceutical and the patient-specific dose kernel. In this study, we consider the uncertainty with which such absorbed dose estimation can be achieved in a clinical environment. METHODS: To calculate the total error of dose estimation we considered the following aspects: The error resulting from computing the time-integrated activity, the difference between the S-value and the patient specific full Monte Carlo simulation, the error from segmenting the volume-of-interest (kidney) and the intrinsic error of the activimeter. RESULTS: The total relative error in dose estimation can amount to 25.0% and is composed of the error of the time-integrated activity 17.1%, the error of the S-value 16.7%, the segmentation error 5.4% and the activimeter accuracy 5.0%. CONCLUSION: Errors from estimating the time-integrated activity and approximations applied to dose kernel computations contribute about equally and represent the dominant contributions far exceeding the contributions from VOI segmentation and activimeter accuracy.

Technical Note: A comparison of point set registration methods for electromagnetic tracking.

PURPOSE: High dose rate brachytherapy applies intense and destructive radiation. A treatment plan defines radiation source dwell positions to avoid irradiating healthy tissue. The study discusses methods to quantify any positional changes of source locations along the various treatment sessions. METHODS: Electromagnetic tracking (EMT) localizes the radiation source during the treatment sessions. But in each session the relative position of the patient relative to the filed generator is changed. Hence, the measured dwell point sets need to be registered onto each other to render them comparable. Two point set registration techniques are compared: a probabilistic method called coherent point drift (CPD) and a multidimensional scaling (MDS) technique. RESULTS: Both enable using EMT without external registration and achieve very similar results with respect to dwell position determination of the radiation source. Still MDS achieves smaller grand average deviations (CPD-rPSR: MD = 2.55 mm, MDS-PSR: MD = 2.15 mm) between subsequent dwell position determinations, which also show less variance (CPD-rPSR: IQR = 4 mm, MDS-PSR: IQR = 3 mm). Furthermore, MDS is not based on approximations and does not need an iterative procedure to track sensor positions inside the implanted catheters. CONCLUSION: Although both methods achieve similar results, MDS is to be preferred over rigid CPD while nonrigid CPD is unsuitable as it does not preserve topology.

Drain Usage in Head and Neck Surgery: A National Survey of Thirty-five Surgeons across Ten Units

Introduction Drain usage is commonplace in head and neck surgery. There is an increasing body of literature disputing their routine placement in certain procedures. The aim of this study is to explore modern-day practice in terms of drain usage and the use of haemostatic agents. Methods A simple questionnaire was devised and sent to 35 ENT Surgeons across 10 units nationally. Results There was an overall response rate of 77.1% (n=27). There was considerable heterogeneity amongst surgeons in terms of indication for insertion, how the decision is made to remove the drain and if any alternative/adjunctive haemostatic agents are being used. Discussion The management of drains is poorly defined and guidelines are lacking. With increased pressure on resources, the risk of infection and discomfort to the patient, further reflection is required to evaluate if careful patient selection rather than habitual drain insertion in every case is more appropriate.

Effects of Preparatory Coaching and Home Practice for Deep Inspiration Breath Hold on Cardiac Dose for Left Breast Radiation Therapy.

AIMS: Deep inspiration breath hold (DIBH) reduces cardiac radiation exposure by creating cardiac-chest wall separation in breast cancer radiotherapy. DIBH requires sustaining chest wall expansion for up to 40 s and involves complex co-ordination of thoraco-abdominal muscles, which may not be intuitive to patients. We investigated the effect of in-advance preparatory DIBH coaching and home practice on cardiac doses. MATERIALS AND METHODS: Successive patients from 1 February 2015 to 31 December 2016 with left-sided breast cancer who underwent tangential field radiotherapy utilising the DIBH technique were included. The study cohort consisted of patients treated by a physician who routinely provided DIBH coaching and home practice instructions at least 5 days before simulation. The control group included non-coached patients under another physician's care. Minimum, maximum and mean cardiac doses and V5, V10 and V30 from DIBH and free breathing simulation computed tomography scans were obtained from the planning system. DIBH and free breathing cardiac doses and volume exposures were compared between the coached and non-coached groups using the two-sample t-test, Fisher's exact test and the Mann-Whitney U-test. RESULTS: Twenty-seven coached and 42 non-coached patients were identified. The DIBH maximum cardiac dose was lower in coached patients at 13.1 Gy compared with 19.4 Gy without coaching (P = 0.004). The percentage cardiac volume exposure in DIBH was lower in coached patients; the DIBH V10 was 0.5% without coaching and 0.1% with coaching (P = 0.005). There was also a trend towards lower DIBH V5 in the coached group compared with the non-coached group (1.2% versus 1.9%, P = 0.071). No significant differences in patient cardiopulmonary comorbidity factors that might influence cardiac doses were found between the groups. CONCLUSIONS: Our results suggest that cardiac dose sparing can potentially be further improved with a 5 day regimen of preparatory DIBH coaching and in-advance home practice before simulation. These hypothesis-generating findings should be confirmed in a larger study.

The effectiveness of prehospital hypertonic saline for hypotensive trauma patients: a systematic review and meta-analysis.

BACKGROUND: The optimal prehospital fluid for the treatment of hypotension is unknown. Hypertonic fluids may increase circulatory volume and mute the pro-inflammatory response of the body to injury and illness. The purpose of this systematic review is to determine whether in patients presenting with hypotension in the prehospital setting (population), the administration of hypertonic saline (intervention), compared to an isotonic fluid (control), improves survival to hospital discharge (outcome). METHODS: Searches were conducted in Medline, Embase, CINAHL, and CENTRAL from the date of database inception to November, 2016, and included all languages. Two reviewers independently selected randomized control trials of hypotensive human participants administered hypertonic saline in the prehospital setting. The comparison was isotonic fluid, which included normal saline, and near isotonic fluids such as Ringer's Lactate. Assessment of study quality was done using the Cochrane Collaborations' risk of bias tool and a fixed effect meta-analysis was conducted to determine the pooled relative risk of survival to hospital discharge. Secondary outcomes were reported for fluid requirements, multi-organ failure, adverse events, length of hospital stay, long term survival and disability. RESULTS: Of the 1160 non-duplicate citations screened, thirty-eight articles underwent full-text review, and five trials were included in the systematic review. All studies administered a fixed 250 ml dose of 7.5% hypertonic saline, except one that administered 300 ml. Two studies used normal saline, two Ringer's Lactate, and one Ringer's Acetate as control. Routine care co-interventions included isotonic fluids and colloids. Five studies were included in the meta-analysis (n = 1162 injured patients) with minimal statistical heterogeneity (I 2  = 0%). The pooled relative risk of survival to hospital discharge with hypertonic saline was 1.02 times that of patients who received isotonic fluids (95% Confidence Interval: 0.95, 1.10). There were no consistent statistically significant differences in secondary outcomes. CONCLUSIONS: There was no significant difference in important clinical outcomes for hypotensive injured patients administered hypertonic saline compared to isotonic fluid in the prehospital setting. Hypertonic saline cannot be recommended for use in prehospital clinical practice for the management of hypotensive injured patients based on the available data. PROSPERO registration # CRD42016053385 .

A tool to automatically analyze electromagnetic tracking data from high dose rate brachytherapy of breast cancer patients.

During High Dose Rate Brachytherapy (HDR-BT) the spatial position of the radiation source inside catheters implanted into a female breast is determined via electromagnetic tracking (EMT). Dwell positions and dwell times of the radiation source are established, relative to the patient's anatomy, from an initial X-ray-CT-image. During the irradiation treatment, catheter displacements can occur due to patient movements. The current study develops an automatic analysis tool of EMT data sets recorded with a solenoid sensor to assure concordance of the source movement with the treatment plan. The tool combines machine learning techniques such as multi-dimensional scaling (MDS), ensemble empirical mode decomposition (EEMD), singular spectrum analysis (SSA) and particle filter (PF) to precisely detect and quantify any mismatch between the treatment plan and actual EMT measurements. We demonstrate that movement artifacts as well as technical signal distortions can be removed automatically and reliably, resulting in artifact-free reconstructed signals. This is a prerequisite for a highly accurate determination of any deviations of dwell positions from the treatment plan.

On the use of multi-dimensional scaling and electromagnetic tracking in high dose rate brachytherapy.

High dose rate brachytherapy affords a frequent reassurance of the precise dwell positions of the radiation source. The current investigation proposes a multi-dimensional scaling transformation of both data sets to estimate dwell positions without any external reference. Furthermore, the related distributions of dwell positions are characterized by uni-or bi-modal heavy-tailed distributions. The latter are well represented by α-stable distributions. The newly proposed data analysis provides dwell position deviations with high accuracy, and, furthermore, offers a convenient visualization of the actual shapes of the catheters which guide the radiation source during the treatment.

On the use of particle filters for electromagnetic tracking in high dose rate brachytherapy.

Modern radiotherapy of female breast cancers often employs high dose rate brachytherapy, where a radioactive source is moved inside catheters, implanted in the female breast, according to a prescribed treatment plan. Source localization relative to the patient's anatomy is determined with solenoid sensors whose spatial positions are measured with an electromagnetic tracking system. Precise sensor dwell position determination is of utmost importance to assure irradiation of the cancerous tissue according to the treatment plan. We present a hybrid data analysis system which combines multi-dimensional scaling with particle filters to precisely determine sensor dwell positions in the catheters during subsequent radiation treatment sessions. Both techniques are complemented with empirical mode decomposition for the removal of superimposed breathing artifacts. We show that the hybrid model robustly and reliably determines the spatial positions of all catheters used during the treatment and precisely determines any deviations of actual sensor dwell positions from the treatment plan. The hybrid system only relies on sensor positions measured with an EMT system and relates them to the spatial positions of the implanted catheters as initially determined with a computed x-ray tomography.

Minimally invasive radiologic techniques in the treatment of uretero-enteric fistulas.

OBJECTIVES: The goal of this study was to assess the efficacy of minimally invasive interventional radiologic (IR) techniques in the management of uretero-enteric fistulae in comparison to established surgical modalities. MATERIALS AND METHODS: Twenty-five patients (16 men, 9 women) with a mean age of 47 (range: 19-77 years) with uretero-enteric fistulae were treated with percutaneous nephrostomy, double "J" stent, radiologic uretero-neocystostomy, and radiologic uretero-pyelocalicostomy. All patients had a single fistula each. Uretero-enteric fistulas were due to direct or iatrogenic trauma in 14 patients (uretero-ileal fistulas, n=6; uretero-colonic fistulas, n=4; uretero-duodenal fistulas, n=2; uretero-pancreatic fistula, n=1; uretero-fallopian tube, n=1), complications of pelvic neoplasms in 4 patients (uretero-sigmoid fistulas, n=4), inflammatory disease in 4 patients (uretero-ileal fistulas, n=2; uretero-sigmoid fistulas, n=2), and avascular necrosis of renal transplants in 3 patients (uretero-sigmoid fistulas, n=3). RESULTS: Drainage by percutaneous nephrostomy and double "J" stent resulted in closure of 8 uretero-enteric fistulae over 7-16 weeks. Four uretero-enteric fistulae obliterated after re-routing urine flow using 3 radiologic uretero-neocystostomies and one IR pyelocalicostomy. In other patients, flow through the fistulae was substantially decreased by five double "J" stents and 3 percutaneous nephrostomies. The duration of inpatient hospitalization was significantly less for patients managed successfully by IR procedures than those treated by surgical modalities, 5.07 versus 10.5 days mean (P<0.05). CONCLUSIONS: IR procedures provided definitive treatment in 48% of uretero-enteric fistulae at significantly reduced inpatient hospitalization and cost. As palliative treatment, it improved the quality of life.

IRF4 and BATF are critical for CD8⁺ T-cell function following infection with LCMV.

CD8(+) T-cell functions are critical for preventing chronic viral infections by eliminating infected cells. For healthy immune responses, beneficial destruction of infected cells must be balanced against immunopathology resulting from collateral damage to tissues. These processes are regulated by factors controlling CD8(+) T-cell function, which are still incompletely understood. Here, we show that the interferon regulatory factor 4 (IRF4) and its cooperating binding partner B-cell-activating transcription factor (BATF) are necessary for sustained CD8(+) T-cell effector function. Although Irf4(-/-) CD8(+) T cells were initially capable of proliferation, IRF4 deficiency resulted in limited CD8(+) T-cell responses after infection with the lymphocytic choriomeningitis virus. Consequently, Irf4(-/-) mice established chronic infections, but were protected from fatal immunopathology. Absence of BATF also resulted in reduced CD8(+) T-cell function, limited immunopathology, and promotion of viral persistence. These data identify the transcription factors IRF4 and BATF as major regulators of antiviral cytotoxic T-cell immunity.

Reactive oxygen species delay control of lymphocytic choriomeningitis virus.

Cluster of differentiation (CD)8(+) T cells are like a double edged sword during chronic viral infections because they not only promote virus elimination but also induce virus-mediated immunopathology. Elevated levels of reactive oxygen species (ROS) have been reported during virus infections. However, the role of ROS in T-cell-mediated immunopathology remains unclear. Here we used the murine lymphocytic choriomeningitis virus to explore the role of ROS during the processes of virus elimination and induction of immunopathology. We found that virus infection led to elevated levels of ROS producing granulocytes and macrophages in virus-infected liver and spleen tissues that were triggered by the nicotinamide adenine dinucleotide phosphate (NADPH) oxidase. Lack of the regulatory subunit p47phox of the NADPH oxidase diminished ROS production in these cells. While CD8(+) T cells exhibited ROS production that was independent of NADPH oxidase expression, survival and T-cell function was elevated in p47phox-deficient (Ncf1(-/-)) mice. In the absence of p47phox, enhanced T-cell immunity promoted virus elimination and blunted corresponding immunopathology. In conclusion, we find that NADPH-mediated production of ROS critically impairs the immune response, impacting elimination of virus and outcome of liver cell damage.

Leucurogin, a new recombinant disintegrin cloned from Bothrops leucurus (white-tailed-jararaca) with potent activity upon platelet aggregation and tumor growth.

Disintegrins and disintegrins-like proteins are able to inhibit platelet aggregation and integrin-mediated cell adhesion. The aim of this study was to produce one disintegrin-like cloned from Bothrops leucurus venom gland and to characterize it regarding biological activity. The recombinant protein was purified by one step procedure involving anion-exchange chromatography (DEAE-cellulose) and presented a molecular mass of 10.4 kDa. The purified protein was able to inhibit platelet aggregation induced by collagen (IC50 = 0.65 µM) and to inhibit growth of Ehrlich tumor implanted in mice by more than 50% after 7 days administration of 10 µg/day. No effects were observed upon adenosine 5'-diphosphate (ADP)-and arachidonic acid (AA)-induced platelet aggregation. The recombinant protein was recognized by an antibody specific for jararhagin one metalloproteinase isolated from Bothrops jararaca venom, and therefore it was named leucurogin. Anti-angiogenesis effect of leucurogin was evaluated by the sponge implant model. After 7 days administration leucurogin inhibited, in a dose dependent way, the vascularization process in the sponge. Leucurogin represents a new biotechnological tool to understand biological processes where disintegrins-like are involved and may help to characterize integrins that can be involved in development and progression of malignant cells.

In cereo and in silico: tissue microarray (TMA) techniques and bioinformatics are thriving forces in medical science and personalized medicine.

OBJECTIVES: Tissue microarray (TMA) techniques are among the most promising developments in biomedicine during the last decade. Bioinformatics techniques are indispensable for storing and processing the masses of data related with tissue archive administration and investigation of raw data. Interrelationship between experimental and computational work will be shown. METHODS: Tissue specimen arrays allow parallel analysis of huge amounts of samples. TMA techniques thus produce enormous masses of raw data, and optimal use of data can only be made using modern bioinformatics techniques based on huge storage systems, scalable multilayer software architecture and high-throughput algorithms for retrieval and statistical processing. Further crucial issues addressed by informatics techniques are specimen identification during the whole processing chain, and anonymization whenever scientific work is performed without regard to a certain patient. RESULTS: TMA supported by bioinformatics methods has helped in identification of biomarkers, mainly in cancer diagnosis. Moreover, it provides powerful means of quality assurance and training in histopathology. CONCLUSIONS: Further statistical analyses seem to be necessary to detect if certain biomarkers are present in nearly all kinds of specimen of the concerned patient, which would allow effective mass screening based on easily accessible specimen. Some investigations showed low dependence on the specimen localization, whereas others suggest to be extremely careful in material selection for the recipient block.

Analyzing time-dependent microarray data using independent component analysis derived expression modes from human macrophages infected with F. tularensis holartica.

The analysis of large-scale gene expression profiles is still a demanding and extensive task. Modern machine learning and data mining techniques developed in linear algebra, like Independent Component Analysis (ICA), become increasingly popular as appropriate tools for analyzing microarray data. We applied ICA to analyze kinetic gene expression profiles of human monocyte derived macrophages (MDM) from three different donors infected with Francisella tularensis holartica and compared them to more classical methods like hierarchical clustering. Results were compared using a pathway analysis tool, based on the Gene Ontology and the MeSH database. We could show that both methods lead to time-dependent gene regulatory patterns which fit well to known TNFalpha induced immune responses. In comparison, the nonexclusive attribute of ICA results in a more detailed view and a higher resolution in time dependent behavior of the immune response genes. Additionally, we identified NFkappaB as one of the main regulatory genes during response to F. tularensis infection.