'Cloudbuster': a Python-based open source application for three-dimensional reconstruction and quantification of stacked biological imaging samples.

Three-dimensional (3D) spheroid cultures are generating increasing interest in cancer research, e.g. for the evaluation of pharmacological effects of novel small molecule inhibitors. This is mainly due to the fact that such 3D structures reflect physiological characteristics of tumours and the cellular microenvironments they reside in more faithfully than two-dimensional (2D) cell cultures; in addition, they allow the reduction of animal experiments while providing significantly relevant human-based models. Quantification of such organoid structures as well as the mainly slice-based acquisition and thus forced 2D representation of 3D spheroids provide a challenge for the interpretation of the associated generated data. Here, we provide a novel open-source workflow to reconstruct a 3D entity from slice-recorded microscopical images with or without treatment with anti-migratory small molecule inhibitors. This reconstruction produces distinct point clouds as basis for subsequent comparison of basic readout parameters using average computer processor, memory and graphics resources within an acceptable time frame. We were able to validate the usefulness of this workflow using 3D data generated by various imaging techniques, including z-stacks from confocal microscopy and histochemically labelled spheroid sectioning, and demonstrate the possibility to accurately characterize inhibitor effects in great detail.

Randomized comparison of synchronous CABG and carotid endarterectomy vs. isolated CABG in patients with asymptomatic carotid stenosis: the CABACS trial.

RATIONALE: High-grade carotid artery stenosis is present in 6-8% of patients undergoing coronary artery bypass graft surgery. Many cardiovascular surgeons advocate staged or synchronous carotid endarterectomy to reduce the high perioperative and long-term risk of stroke associated with multivessel disease. However, no randomized trial has assessed whether a combined synchronous or staged carotid endarterectomy confers any benefit compared with isolated coronary artery bypass grafting in these patients. AIMS: The objective of this study is to compare the safety and efficacy of isolated coronary artery bypass grafting vs. synchronous coronary artery bypass grafting and carotid endarterectomy in patients with asymptomatic high-grade carotid artery stenosis. DESIGN: Coronary Artery Bypass graft surgery in patients with Asymptomatic Carotid Stenosis (CABACS) is a randomized, controlled, open, multicenter, group sequential trial with two parallel arms and outcome adjudication by blinded observers. Patients with asymptomatic high-grade carotid stenosis scheduled for elective coronary artery bypass grafting will be assigned to either isolated coronary artery bypass grafting or synchronous coronary artery bypass grafting and carotid endarterectomy by 1 : 1 block-stratified randomization with three different stratification factors (age, gender, modified Rankin scale). STUDY: The trial started in December 2010 aiming at recruiting 1160 patients in 25 to 30 German cardiovascular centers. The composite primary efficacy end point is the number of strokes and deaths from any cause (whatever occurs first) within 30 days after operation. A 4·5% absolute difference (4% compared to 8·5%) in the 30-day rate of the above end points can be detected with >80% power. OUTCOMES: The results of this trial are expected to provide a basis for defining an evidence-based standard and will have a wide impact on managing this disease.

A pilot study of bendamustine in elderly patients with high-risk MDS and AML.

We examined the efficacy of bendamustine in 15 pretreated patients (12 men, 3 women, median age 69 years) with acute myeloid leukaemia (AML) or myelodysplastic syndromes (MDS) 3 AML, 5 sAML, 5 CMML II, 1 RAEB II. Patients belonged to the following cytogenetic groups: 3 complex abnormal karyotypes, 7 normal karyotypes, 1 case with 20q- as sole anomaly and 4 single aberrations. The patients received in median two cycles of bendamustine (range 1-5) with a dose of 100 mg/m(2) at Day 1 + 2 (repeated after 28 days). Nine of 15 patients had no side effects of the treatment, six patients suffered from vomiting and epigastric pain as adverse effects of bendamustine. According to the IWG criteria, no complete remission or reduction of transfusions frequency have been observed. Three patients showed no response, one patient with AML died due to progressive disease. In 11 of 12 patients with initial leukocytosis (median 68,975 microl(-1), range 24,000-149,000 microl(-1)), a significant reduction of leukocytosis was achieved with bendamustine with a median duration of 4 weeks. In summary, treatment with bendamustine in patients with high-risk MDS or sAML with leukocytosis can result in a significant reduction of leukocytes, but fails to achieve hematological responses or improvement of transfusions dependency.

[Evaluation of myocardial viability with contrast-enhanced magnetic resonance imaging--comparison of the late enhancement technique with positronemission tomography]. / Myokardiale Vitalitätsdiagnostik mit kontrastverstärkter Magnetresonanztomographie - Vergleich des "late enhancement"-Konzepts mit der Positronen-Emissions-Tomographie.

PURPOSE: To compare contrast-enhanced magnetic resonance imaging (MRI) and positron emission tomography (PET) in the evaluation of myocardial viability. METHODS: [ (18)F]-FDG-PET, [ (201)Tl]-TlCl-SPECT and contrast-enhanced MRI were performed in 29 patients with proven coronary artery disease and impaired left ventricular function to assess myocardial viability. MRI scans were done on a 1.5 T scanner (Magnetom Sonata, Siemens, Germany). After the steady-state free precession cine study, 0.2 mmol/kg BW of Gd-DPTA (Magnevist(R), Schering, Germany) were administered i. v. For the detection of "late enhancement" (LE) indicating scar, left ventricular long axes and contiguous short axis slices of 8 mm thickness were scanned using an inversion recovery turbo gradient echo sequence (TR 8.0 ms; TE 4.0 ms; TI 180 - 240 ms; FA 20 degrees ). The evaluation of LE and FDG uptake in PET with perfusion defect in SPECT was done using an 8 (basal, mid) and 4 (apical) segment model in all short axes to cover the entire ventricle. The transmural extent of LE was assessed using a 4-point score system. Comparison between the two modalities was performed on a segmental basis. RESULTS: A total of 1753 segments were assessed. In MRI, 40 % of the segments showed myocardial scar, whereas PET revealed impaired uptake in 25 %. MRI obtained a very low interobserver variability in detecting myocardial scar (kappa 0.92). Using PET as the standard of reference in the segmental comparison, contrast-enhanced MRI yielded a sensitivity of 84 % and a specificity of 76 % for the detection of scar. 18 % of all segments showed LE but normal FDG uptake, 83 % of them referred to subendocardial scars. CONCLUSIONS: There is close agreement between contrast-enhanced MRI and PET in detecting transmural myocardial scars. Superior spatial resolution enables MRI to detect and quantify even subendocardial scar. Therefore, larger studies using functional recovery after revascularisation as an endpoint have to prove whether MRI might replace PET as the standard of reference in the assessment of myocardial viability.

Characterization of cationic vector-based gene delivery vehicles using isothermal titration and differential scanning calorimetry.

Within the past 10 years, major advances in the design and development of differential scanning calorimeters (DSC) (1) and isothermal titration calorimeters (ITC) (2) have resulted in an unparalleled level of sensitivity, stability, and reproducibility in calorimetric measurements of large molecules. These improvements have allowed the thermal stability and ligand binding processes of biological macromolecules to be thermodynamically characterized with speed, accuracy, and convenience. With their increasing commercial availability, experiments that were previously limited to specialist calorimetry laboratories can now be routinely performed by most investigators.

Proliferation pattern changes in the zebrafish brain from embryonic through early postembryonic stages.

Proliferating cell nuclear antigen (PCNA)-immunohistochemistry was used for demonstrating the spatiotemporal course of proliferation in the brains of embryonic (24 h) through postembryonic (5 days) zebrafish (Danio rerio). Parallel series of the same stages prepared according to the combined Bodian fiber silver-stain/cresyl Nissl-stain were used for improved morphogenetic analysis (i.e., in detecting critical neuroanatomical landmarks). Starting from an essentially ubiquituous proliferation throughout the neural tube before 24 h, PCNA-immunoreactive cells become successively more restricted to a subset of gray matter cells around 48 h and even more distinct proliferation zones become apparent around 72 h. Both hindbrain and forebrain reveal a segmental organization with regard to the distribution of proliferation zones, but the rhombomeric pattern of PCNA-immunoreactive cells emerging between 48 h and 72 h precedes a similar prosomeric pattern by about 48 h. Two divisions of the midbrain-hindbrain boundary are described here morphologically and both are demonstrated to show sustained proliferation throughout the investigated time frame. In contrast, proliferation in the adjacent mesencephalic and cerebellar domains is rapidly down-regulated during the first 5 days of development.

Relapsing polychondritis in childhood--case report and short review.

Relapsing polychondritis (RP) is a disease of unknown etiology and it is characterized by inflammation of the cartilage. While the clinical picture of RP in adults is well described, RP in childhood is poorly documented. We describe a young girl presenting with acute dyspnea, stridor and polyarthritis. The diagnosis of RP was made 2 years after first presentation, when auricular chondritis occurred. Based on a MEDLINE search, reports on RP in childhood were reviewed. The frequency of chondritis and systemic manifestations of RP in children was compared to data in adults and found to be very similar. RP in childhood can be a life-threatening and debilitating disease.

Treatment-resistant expansion of CD8+CD28-cells in pediatric HIV infection.

There is a disease stage-dependent loss of CD28 expression on T cells in HIV-infected children. In this study, T cell recovery, in particular CD28 expression on T cells, was analyzed after initiation of highly active antiretroviral therapy in a group of eight mostly treatment-naive HIV-infected children. Plasma HIV-RNA levels were recorded, and numbers of CD4, CD8, CD4+CD28+, and CD8+CD28+ cells were determined by two-color flow cytometry. Values after 12 mo of therapy were compared with age-matched, seronegative control subjects. CD4 recovery to subnormal values was observed in all children. CD8+CD28+ cells recovered and were within the normal range after 12 mo of therapy (patients, 703 +/- 250 cells/microL; controls, 789 +/- 269 cells/microL), whereas CD8+CD28- cells (546 +/- 269 cells/microL) remained significantly expanded compared with age-matched controls (140 +/- 35 cells/microL). Expansions of CD8+CD28- cells persisted even in cases with long-term suppression of viral replication. Highly active antiretroviral therapy in HIV-infected children induces substantial but incomplete T cell recovery.

Gastric and duodenal features of meals mediate controls of liquid gastric emptying during fill in rhesus monkeys.

To study the dynamics of liquid gastric emptying in rhesus monkeys under conditions that simulated gastric fill during a meal, we measured the gastric emptying of liquid glucose at various concentrations and volumes when administered intragastrically at rates ranging from 12.5 to 37.5 ml/min. Glucose gastric emptying was faster during than following the period of gastric fill. At a single glucose concentration, volume infused rather than the rate of filling determined the volume emptied. Lower glucose concentrations emptied more slowly than physiological saline. As glucose concentration increased, emptying during fill slowed. Duodenal glucose infusions greatly slowed the rate of saline emptying during fill, demonstrating duodenal feedback control. Although casein hydrolosate emptied more rapidly than glucose, the dynamics of volume and concentration dependency and the role of duodenal feedback were similar. These data reveal that both gastric volume and duodenal negative feedback controls important in gastric emptying following stomach filling also contribute to its control during fill.

Effect of conformation on the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH to its cyclic imide degradation product.

The objective of this study was to explain the increased propensity for the conversion of cyclo-(1,7)-Gly-Arg-Gly-Asp-Ser-Pro-Asp-Gly-OH (1), a vitronectin-selective inhibitor, to its cyclic imide counterpart cyclo-(1,7)-Gly-Arg-Gly-Asu-Ser-Pro-Asp-Gly-OH (2). Therefore, we present the conformational analysis of peptides 1 and 2 by NMR and molecular dynamic simulations (MD). Several different NMR experiments, including COSY, COSY-Relay, HOHAHA, NOESY, ROESY, DQF-COSY and HMQC, were used to: (a) identify each proton in the peptides; (b) determine the sequential assignments; (c) determine the cis-trans isomerization of X-Pro peptide bond; and (d) measure the NH-HCalpha coupling constants. NOE- or ROE-constraints were used in the MD simulations and energy minimizations to determine the preferred conformations of cyclic peptides 1 and 2. Both cyclic peptides 1 and 2 have a stable solution conformation; MD simulations suggest that cyclic peptide 1 has a distorted type I beta-turn at Arg2-Gly3-Asp4-Ser5 and cyclic peptide 2 has a pseudo-type I beta-turn at Ser5-Pro6-Asp7-Gly1. A shift in position of the type I beta-turn at Arg2-Gly3-Asp4-Ser5 in peptide 1 to Ser5-Pro6-Asp7-Gly1 in peptide 2 occurs upon formation of the cyclic imide at the Asp4 residue. Although the secondary structure of cyclic peptide 1 is not conducive to succinimide formation, the reaction proceeds via neighbouring group catalysis by the Ser5 side chain. This mechanism is also supported by the intramolecular hydrogen bond network between the hydroxyl side chain and the backbone nitrogen of Ser5. Based on these results, the stability of Asp-containing peptides cannot be predicted by conformational analysis alone; the influence of anchimeric assistance by surrounding residues must also be considered.

The effect of conformation on the solution stability of linear vs. cyclic RGD peptides.

The objective of this study was to evaluate the relationship between conformational flexibility and solution stability of a linear RGD peptide (Arg-Gly-Asp-Phe-OH; 1) and a cyclic RGD peptide (cyclo-(1, 6)-Ac-Cys-Arg-Gly-Asp-Phe-Pen-NH2; 2); as a function of pH. Previously, it was found that cyclic peptide 2 was 30-fold more stable than linear peptide 1. Therefore, this study was performed to explain the increase in chemical stability based on the preferred conformation of the peptides. Molecular dynamics simulations and energy minimizations were conducted to evaluate the backbone flexibility of both peptides under simulated pH conditions of 3, 7 and 10 in the presence of water. The reactive sites for degradation for both molecules were also followed during the simulations. The backbone of linear peptide 1 exhibited more flexibility than that of cyclic peptide 2, which was reflected in the rotation about the phi and psi dihedral angles. This was further supported by the low r.m.s. deviations of the backbone atoms for peptide 2 compared with those of peptide 1 that were observed among structures sampled during the molecular dynamics simulations. The presence of a salt bridge between the side chain groups of the Arg and Asp residues was also indicated for the cyclic peptide under simulated conditions of neutral pH. The increase in stability of the cyclic peptide 2 compared with the linear peptide 1, especially at neutral pH, is due to decreased structural flexibility imposed by the ring, as well as salt bridge formation between the side chains of the Arg and Asp residues in cyclic peptide 2. This rigidity would prevent the Asp side chain carboxylic acid from orienting itself in the appropriate position for attack on the peptide backbone.

Solution stability of linear vs. cyclic RGD peptides.

Arg-Gly-Asp (RGD) peptides contain an aspartic acid residue that is highly susceptible to chemical degradation and leads to the loss of biological activity. Our hypothesis is that cyclization of RGD peptides via disulphide bond linkage can induce structural rigidity, thereby preventing degradation mediated by the aspartic acid residue. In this paper, we compared the solution stability of a linear peptide (Arg-Gly-Asp-Phe-OH; 1) and a cyclic peptide (cyclo-(1, 6)-Ac-Cys-Arg-Gly-Asp-Phe-Pen-NH2; 2) as a function of pH and buffer concentration. The decomposition of both peptides was studied in buffers ranging from pH 2-12 at 50 degrees C. Reversed-phase HPLC was used as the main tool in determining the degradation rates and pathways of both peptides. Fast atom bombardment mass spectrometry (FAB-MS), electrospray ionization mass spectrometry (ESI-MS), matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry, liquid chromatography-mass spectrometry (LC-MS), and one- and two-dimensional nuclear magnetic resonance spectroscopy (NMR) were used to characterize peptides 1 and 2 and their degradation products. In addition, co-elution with authentic samples was used to identify degradation products. Both peptides displayed pseudo-first-order kinetics at all pH values studied. The cyclic peptide 2 appeared to be 30-fold more stable than the linear peptide 1 at pH 7. The degradation mechanisms of linear (1) and cyclic (2) peptides primarily involved the aspartic acid residue. However, above pH 8 the stability of the cyclic peptide decreased dramatically due to disulphide bond degradation. Both peptides also exhibited a change in degradation mechanism upon an increase in pH. The increase in stability of cyclic peptide 2 compared to linear peptide 1, especially at neutral pH, may be due to decreased structural flexibility imposed by the ring. This rigidity would prevent the Asp side chain carboxylic acid from orientating itself in the appropriate position for attack on the peptide backbone.

Endogenous CCK in the control of gastric emptying of glucose and maltose.

A role for endogenous cholecystokinin (CCK) in the control of gastric emptying of liquid glucose and maltose test meals in rhesus monkeys was assessed. Intragastric administration of a dose range (10-100 micrograms/kg) of the CCKA receptor antagonist devazepide produced a dose dependent acceleration of the emptying of 100 ml 300 mOsm test meals of glucose and maltose but had no effect on the emptying of a hyperosmotic (750 mOsm) NaCl solution. At the 100 micrograms/kg dose, the emptying of glucose and maltose meals were as rapid as the emptying of physiological NaCl. These data expand the demonstrated role of endogenous CCK in the slowing of gastric emptying of nutrients in rhesus monkeys to carbohydrates and suggest that previous negative results were due to the hyperosmotic nature of the glucose solutions.

Activation of protein kinase C accelerates contraction kinetics of airway smooth muscle.

Contraction kinetics of isolated rat tracheal smooth muscle were studied by analysing the increase of force subsequent to force-inhibiting passive length changes lasting 1 s (100 Hz, sinus, 5% of muscle length). Compared with carbachol activation, phorboldibutyrate (PDBu)-induced stimulation of protein kinase C (PKC) demonstrated no significant difference in the extent of force development in the polarized preparation [mean peak force 9.16 +/- 0.37 mN (carbachol) vs. 9.12 +/- 0.37 mN (PDBu)]. However, the time constant calculated for the slow component of post-vibration force recovery was 6.40 +/- 0.29 s after addition of PDBu vs. 22.39 +/- 1.40 s during carbachol activation, indicating a significant phorbol ester-induced acceleration of the cross-bridge cycling rate. In the K-depolarized preparation, treatment with 26.4 microM indolactam (IL) to activate PKC produced muscle relaxation (9.94 +/- 0.16 mN measured 0-30 min after the onset of depolarization vs. 4.13 +/- 0.05 mN measured during 30-60 min of IL treatment). Again, even in the presence of high sarcoplasmic Ca2+ resulting from tonic depolarization, PKC activation was associated with a distinct diminution of the time constant (25.99 +/- 0.79 s during the first 30 min of depolarization vs. 10.32 +/- 0.21 s during 30-60 min of IL treatment). In contrast, addition of 0.035 microM verapamil, 1.5 microM isoproterenol, and 32 microM dibutyryl-cAMP to the bathing medium induced relaxation without affecting the rate of post-vibration force recovery. The results suggest that the calcium-dependent signal cascade (agonist receptor/inositol trisphosphate/ Ca(2+)-calmodulin/myosin light chain kinase) hardly affects the regulation of contraction kinetics in the tonically activated intact smooth muscle preparation. PKC stimulation, however, accelerates actin/myosin interaction kinetics, possibly by inhibition of phosphatase(s).