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TRENTOOL : an open source toolbox to estimate neural directed interactions with transfer entropy
(2011)
To investigate directed interactions in neural networks we often use Norbert Wiener's famous definition of observational causality. Wiener’s definition states that an improvement of the prediction of the future of a time series X from its own past by the incorporation of information from the past of a second time series Y is seen as an indication of a causal interaction from Y to X. Early implementations of Wiener's principle – such as Granger causality – modelled interacting systems by linear autoregressive processes and the interactions themselves were also assumed to be linear. However, in complex systems – such as the brain – nonlinear behaviour of its parts and nonlinear interactions between them have to be expected. In fact nonlinear power-to-power or phase-to-power interactions between frequencies are reported frequently. To cover all types of non-linear interactions in the brain, and thereby to fully chart the neural networks of interest, it is useful to implement Wiener's principle in a way that is free of a model of the interaction [1]. Indeed, it is possible to reformulate Wiener's principle based on information theoretic quantities to obtain the desired model-freeness. The resulting measure was originally formulated by Schreiber [2] and termed transfer entropy (TE). Shortly after its publication transfer entropy found applications to neurophysiological data. With the introduction of new, data efficient estimators (e.g. [3]) TE has experienced a rapid surge of interest (e.g. [4]). Applications of TE in neuroscience range from recordings in cultured neuronal populations to functional magnetic resonanace imaging (fMRI) signals. Despite widespread interest in TE, no publicly available toolbox exists that guides the user through the difficulties of this powerful technique. TRENTOOL (the TRansfer ENtropy TOOLbox) fills this gap for the neurosciences by bundling data efficient estimation algorithms with the necessary parameter estimation routines and nonparametric statistical testing procedures for comparison to surrogate data or between experimental conditions. TRENTOOL is an open source MATLAB toolbox based on the Fieldtrip data format. ...
Objective: Establishment of an immunocompetent mouse model representing the typical progressive stages observed in malignant human gliomas for the in vivo evaluation of novel target-specific regimens.
Methods: Isolated clones from tumours that arose spontaneously in GFAP-v-src transgenic mice were used to develop a transplantable brain tumour model in syngeneic B6C3F1 mice. STAT3 protein was knocked down by infection of tumour cells with replication-defective lentivirus encoding STAT3-siRNA. Apoptosis is designed to be induced by soluble recombinant TRAIL + chemical Bcl-2/Bcl-xL inhibitors.
Results: Striatal implantation of 105 mouse tumour cells resulted in the robust development of microscopically (2 – 3 mm) infiltrating malignant gliomas. Immunohistochemically, the gliomas displayed the astroglial marker GFAP and the oncogenic form of STAT3 (Tyr-705-phosphorylated) which is found in many malignancies including gliomas. Phosphorylated STAT3 was particularly prominent in the nucleus but was also found at the plasma membrane of peripherally infiltrating glioma cells. To evaluate the role of STAT3 in tumour progression, we stably expressed siRNA against STAT3 in several murine glioma cell lines. The effect of STAT3 depletion on proliferation, invasion and survival will be first assessed in vitro and subsequently after transplantation in vivo. Upstream and downstream components of the STAT3 signalling pathway as well as possible non-specific side effects of STAT3-siRNA expression after lentiviral infection will be examined, too.
Conclusions: Its high rate of engraftment, its similarity to the malignant glioma of origin, and its rapid locally invasive growth should make this murine model useful in testing novel therapies for malignant gliomas.
Einleitung: Es wurden die Leistungen beim Verstehen im Störgeräusch von CI-Patienten mit unterschiedlichen Implantattypen verglichen. Der TEMPO+ Sprachprozessor (MED-EL, Implantat C40+) verwendet ein Mikrophon mit Kugelcharakteristik, während der ESPrit 3G Prozessor (COCHLEAR, Implantat CI24R(CA)) mit einem frontal ausgelegten Richtmikrophon ausgestattet ist.
Methode: Von den zwei untersuchten Patientengruppen (n=20) war eine mit einem C40+ Implantat (MED-EL, Innsbruck), die andere mit dem CI24RCA Implantat (Cochlear, Melbourne) versorgt. Es wurde die S0N180 Lautsprecheranordnung im Freifeld für den HSM-Test (Hochmair, Schulz und Moser, 1997) und die S0N0 Anordnung für den Oldenburger Satztest (Wagener, Kühnel und Kollmeier, 1999) verwendet. Der OLSA wurde mit festem Sprachpegel (65 dB SPL) und adaptivem Störgeräusch durchgeführt. Der HSM-Satztest wurde bei Signal-/ Rauschverhältnissen von 15 dB, 10 dB, 5 dB, 0dB sowie ohne Störgeräusch durchgeführt.
Ergebnisse: Im HSM-Satztest (S0N180) wurden signifikant bessere Leistungen beim Verstehen im Störgeräusch für die Gruppe mit dem Richtmikrophon nachgewiesen. Im Oldenburger Satztest zeigten sich keine signifikanten Unterschiede.
Schlussfolgerungen: Im Vergleich zu einem Mikrophon mit Kugelcharakteristik verbessert ein Richtmikrophon das Sprachverstehen in Situationen, in denen die Sprache frontal und der Störschall von hinten dargeboten werden.
Background The detection of the new Coranavirus (CoV) causing agent of the severe acute respiratory syndrome (SARS) for diagnostic purposes is still a critical step in prevention of secondary hospital infections. In this respect the PCR for SARS diagnostic is the fastest and most sensitive method and was published very early after the description of the new pathogen by different groups. To evaluate the quality and sensitivity of the SARS PCR performed in diagnostic laboratories all over the world an external quality assurance (EQA) for SARS PCR was initiated by the WHO, the European Network for Diagnostics of "Imported" Viral Diseases (ENIVD) and the Robert Koch-Institut. Methods Therefore 10 samples of inactivated SARS CoV strains isolated in Frankfurt and Hong Kong in different dilutions and negative controls were prepared. The freeze dried samples were send by mail to 62 different laboratories, in 37 countries in Europe and Israel (35), Asia (11), The Americas (11), Australia and New Zealand (4) and Africa (1). The results were returned by email or fax 1 week (13), 2 weeks (14), 3 weeks (6) and later (29) after receiving the material which does not mimic at all the possible speed of this fast method. But this was not considered in the evaluation of these first SARS EQA. Results 44 laboratories showed good or excellent results (26 = 100%, 18 = 90%) and even the 14 laboratories which archived only 80% (10) or 70% (4) correct results are mostly lacking sensitivity. The results of the other 4 laboratories show basic problems in regard to sensitivity, specificity and consistency of results and must be overcome as soon as possible. 4 laboratories seem to have problems with the specificity finding a positive signal in negative samples. The different methods used for preparation of the SARS CoV genome and diagnostic PCR test procedure used by the participating laboratories will be discussed in more detail in the presentation. Conclusion However, in contrast to previous EQAs for Ebola, Lassa and Orthopoxviruses the quality of PCR results was rather good which might be caused by the early publication and distribution of well developed PCR methods. An EQA for evaluation of SARS specific serology is still ongoing, first results will be available beginning of April 2004.
Background and Aim: In Germany, the discharge medication is usually reported to the general practitioner (GP) by an inital short report (SR) /notification (handed over to the patient) and later by a more detailed discharge letter (DL) of the hospital.
Material and Method: We asked N=536 GPs (from Frankfurt/Main and Luebeck) after the typical report format of their patients discharge medication by the local hospitals. The questionnaire asked for 26 items covering (1) the designation of the medication (brand name, generic name) in SR and DL, (2) further specifications e.g. possibilities of generic substitution or supervision of sensible medications, (3) reasons why GPs do not follow the hospitals recommendations and (4) possibilities for an improvement in the medication-related communication between GP and hospitals.
Results: 39% GPs responded sufficiently to the questionnaire. The majority of the GPs (82%) quoted that in the SR only brand names are given (often or ever) and neither the generic name or any further information on generic substitution is available (seldom or never). 65% of the responders quoted that even in the DL only brand names are given. Only 41% of the responders quoted that further treatment relevant specifications are given (often or ever). 95% responded that new medications or change of custom medication is seldom or never explained in the DL and GP were not explicitly informed about relevant medication changes. 58% of the responders quoted economic reasons for re-adjustment of the discharge medication e.g. by generic substitution. The majority of responders (83%) are favouring (useful or very useful) a pre-discharge information (e.g. via fax) about the medication and 54% a hot-line to some relevant person in the hospital when treatment problems emerge. 67% of the responders quoted in favour of regular meetings between GPs and hospital doctors regarding actual pharmacotherapy.
Conclusion: In conclusion, our survey pointed to marked deficiencies in reporting the discharge medication to GPs.
Conflict of interest: None
The nervous system probably cannot display macroscopic quantum (i.e. classically impossible) behaviours such as quantum entanglement, superposition or tunnelling (Koch and Hepp, Nature 440:611, 2006). However, in contrast to this quantum "mysticism" there is an alternative way in which quantum events might influence the brain activity. The nervous system is a nonlinear system with many feedback loops at every level of its structural hierarchy. A conventional wisdom is that in macroscopic objects the quantum fluctuations are self-averaging and thus not important. Nevertheless this intuition might be misleading in the case of nonlinear complex systems. Because of a high sensitivity to initial conditions, in chaotic systems the microscopic fluctuations may be amplified upward and thereby affect the system’s output. In this way stochastic quantum dynamics might sometimes alter the outcome of neuronal computations, not by generating classically impossible solutions, but by influencing the selection of many possible solutions (Satinover, Quantum Brain, Wiley & Sons, 2001). I am going to discuss recent theoretical proposals and experimental findings in quantum mechanics, complexity theory and computational neuroscience suggesting that biological evolution is able to take advantage of quantum-computational speed-up. I predict that the future research on quantum complex systems will provide us with novel interesting insights that might be relevant also for neurobiology and neurophilosophy.
Meeting Abstract : Gesellschaft für Arzneimittelanwendungsforschung und Arzneimittelepidemiologie e.V. (GAA). 17. Jahrestagung der Gesellschaft für Arzneimittelanwendungsforschung und Arzneimittelepidemiologie. Osnabrück, 25.-26.11.2010.
ntroduction: Several drugs require dose adjustment in patients with impaired renal function, which however, often goes undetected. Serum creatinine may be normal in patients while renal function is already reduced. The estimated GFR (eGFR) allows a more precise evaluation of the renal function. This study was carried out in a group practice for family medicine, in Frankfurt/ Main, Germany. The exploration aimed at investigating if patients with renal insufficiency were recognised and if their prescriptions were appropriate in terms of dose adjustment or contra-indications.
Methods: In patients (>65yrs) with renal insufficiency (creatinine clearance <60 ml/min), their prescribed medication was retrospectively explored (Observation period 1.1.2008 to 1.4.2009). The Cockroft-Gault formula was used as estimate for the eGFR, using a creatinine value from the patient’s charts. In 90 patients, a second eGFR could be estimated from a second creatinine value obtained within 3-6 months. The recommended dose of each prescription in the SmPC (Fachinformation“) was compared to the dose that had been actually prescribed.
Results: Out of 232 consecutively patients >65 yrs, 102 had an eGFR <60 ml/min, 16 of these had an eGFR <30 ml/min. The eGFR was closely correlated (r2=0.81) with an independent second eGFR. Out of these 102 patients, 48 had a serum creatinine level within the normal range. Renal adjustment was required in 263 of a total of 613 prescriptions. 72 prescriptions in a total of 45 patients were not appropriately adjusted (32) or prescribed despite a contraindication (40). For chronic prescriptions, metformin, ramipril, enalapril, HCTZ, and spironolactone accounted for 70% of inappropriate dosing; the magnitude of misdosing was 1.5 to 4 fold (median 2). 9 temporary prescriptions (of a total of 60 prescriptions) in 8 patients were not adjusted (cefuroxim, cefpodoxim, levofloxacin). We could not prove that patients with normal serum creatinine had a higher rate of inappropriate dosing than those with already elevated creatinine.
Discussion and conclusion: In this GP practice, we have demonstrated a considerable prevalence of inappropriate dosing in patients with impaired renal function. It remains to be elucidated whether surveillance of appropriate dosing in renal impairment can be optimized e.g. with CPOE.
Background: Undergoing systemic inflammation, the innate immune system releases excessive proinflammatory mediators, which finally can lead to organ failure. Pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs) and NOD-like receptors (NLRs), form the interface between bacterial and viral toxins and innate immunity. During sepsis, patients with diagnosed adrenal gland insufficiency are at high risk of developing a multiorgan dysfunction syndrome, which dramatically increases the risk of mortality. To date, little is known about the mechanisms leading to adrenal dysfunction under septic conditions. Here, we investigated the sepsis-related activation of the PRRs, cell inflammation, and apoptosis within adrenal glands.
Methods: Two sepsis models were performed: the polymicrobial sepsis model (caecal ligation and puncture (CLP)) and the LTA-induced intoxication model. All experiments received institutional approval by the Regierungspräsidium Darmstadt. CLP was performed as previously described [1], wherein one-third of the caecum was ligated and punctured with a 20-gauge needle. For LTA-induced systemic inflammation, TLR2 knockout (TLR2-/-) and WT mice were injected intraperitoneally with pure LTA (pLTA; 1 mg/kg) or PBS for 2 hours. To detect potential direct adrenal dysfunction, mice were additionally injected with adrenocorticotropic hormone (ACTH; 100 μg/kg) 1 hour after pLTA or PBS. Adrenals and plasma samples were taken. Gene expressions in the adrenals (rt-PCR), cytokine release (multiplex assay), and the apoptosis rate (TUNEL assay) within the adrenals were determined.
Results: In both models, adrenals showed increased mRNA expression of TLR2 and TLR4, various NLRs, cytokines as well as inflammasome components, NADPH oxidase subunits, and nitric oxide synthases (data not shown). In WT mice, ACTH alone had no effect on inflammation, while pLTA or pLTA/ACTH administration showed increased levels of the cytokines IL-1β, IL-6, and TNFα. TLR2-/- mice indicated no response as expected (Figure 1, left). Interestingly, surviving CLP mice showed no inflammatory adrenal response, whereas nonsurvivors had elevated cytokine levels (Figure 1, right). Additionally, we identified a marked increase in apoptosis of both chromaffin and steroid-producing cells in adrenal glands obtained from mice with sepsis as compared with their controls (Figure 2).
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Conclusion: Taken together, sepsis-induced activation of the PRRs may contribute to adrenal impairment by enhancing tissue inflammation, oxidative stress and culminate in cellular apoptosis, while mortality seems to be associated with adrenal inflammation.
Background: Nerve injury induced protein 1 (Ninjurin 1 (Ninj1)) was first identified in Schwann cells and neurons contributing to cell adhesion and nerve regeneration. Recently, the role of Ninj1 has been linked to inflammatory processes in the central nervous system where functional repression reduced leukocyte infiltration and clinical disease activity during experimental autoimmune encephalomyelitis in mice [1]. But Ninj1 is also expressed outside the nervous system in various organs such as the liver and kidney as well as on leukocytes [2,3]. Therefore, we hypothesized that Ninj1 contributes to inflammation in general; that is, also outside the nervous system, with special interest in the pathogenesis of sepsis.
Methods: Ninj1 was repressed by transfecting HMEC-1 cells, a human dermal microvascular endothelial cell line with siRNA targeting Ninj1 (siNinj1) or a negative control (siC). Subsequently, cells were stimulated with 100 ng/ml LPS (TLR4 agonist), 3 μg/ml LTA (TLR2 agonist) or 100 n/ml poly(I:C) (TLR3 agonist) for 3 hours. The inflammatory response was analyzed by real-time PCR. In addition, transmigration of neutrophils across a HMEC-1 monolayer was measured using transwell plates (pore size 3 μm).
Results: Repression of Ninj1 by siRNA reduced Ninj1 mRNA expression in HMEC about 90% (Figure 1A). Reduced Ninj1 expression decreased neutrophil migration to 62.5% (Figure 1B) and TLR signaling. In detail, knockdown of Ninj1 significantly reduced TLR-2 and TLR-4 triggered expression of ICAM-1 and IL-6 (Figure 1C,D) while poly(I:C)-induced expression was only slightly reduced. To analyze a more specific TLR-3 target, we measured IP-10 mRNA expression, which was also significantly reduced in siNinj1-transfected cells (Figure 1E).
Conclusion: Our in vitro data strongly indicated that Ninj1 is involved in regulation of TLR signaling and therewith contributes to inflammation. In vivo experiments will clarify its impact on systemic inflammation.