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Abstract Prostate segmentation is a substantial factor in the diagnostic pathway of suspicious prostate lesions. Medical doctors are assisted by computer-aided detection and diagnosis systems systems and methods derived from artificial intelligence deep learning-based systems have to be trained on existing data. Especially freely available labeled prostate magnetic resonance imaging data is rare. With regard to this problem, we show a method to combine two existing small datasets to form a bigger one. We present a data processing pipeline consisting of a cascaded network architecture that is able to perform multi-label semantic segmentation, hence, capable of classifying each pixel in a $$\textrm{T}_{2}$$ T 2 -weighted image not only to one class but to a subset of the prostate zones and classes of interest. This delivers richer information such as overlapping zones that are key to medical radiological examination. Additionally, we describe how to integrate expert knowledge in our deep learning system. To increase data variety for training and evaluation we use image augmentation on our two datasets—a freely available dataset and our new open-source dataset. To combine the datasets we denoise the contourings in our dataset by using an effective yet simple algorithm based on standard computer vision methods only. The performance of the presented methodology is compared and evaluated using the dice score metric and 5-fold cross-validation on all datasets. Although we trained on tiny datasets our method achieves excellent segmentation quality and is even able to detect prostate cancer. Our method to combine the two datasets reduces segmentation errors and increases data variety. The proposed architecture significantly improves performance by including expert knowledge via feature-map concatenation. On the initiative for collaborative computer vision benchmarking dataset we achieve on average dice scores of approximately 91% for the whole prostate gland, 67% for the peripheral zone and 75% for the prostate central gland. We find that image augmentation except contrast limited adaptive histogram equalisation did not have much influence on the segmentation quality. Derived and enhanced from existing methods we present an approach that is able to deliver multi-label semantic segmentation results for prostate magnetic resonance imaging. This approach is simple and could be applied to other applications of deep learning as well. It improves the segmentation results by a large margin. Once tweaked to the data, our denoising and combination algorithm delivers robust and accurate results even on data with segmentation errors.

Abstract Retinoblastoma are childhood eye tumors arising from retinal precursor cells. Two distinct retinoblastoma subtypes with different clinical behavior have been described based on gene expression and methylation profiling. Using consensus clustering of DNA methylation analysis from 61 retinoblastomas, we identify a MYCN-driven cluster of subtype 2 retinoblastomas characterized by DNA hypomethylation and high expression of genes involved in protein synthesis. Subtype 2 retinoblastomas outside the MYCN-driven cluster are characterized by high expression of genes from mesodermal development, including NKX2-5. Knockdown of MYCN expression in retinoblastoma cell models causes growth arrest and reactivates a subtype 1-specific photoreceptor signature. These molecular changes suggest that removing the driving force of MYCN oncogenic activity rescues molecular circuitry driving subtype 1 biology. The MYCN-RB gene signature generated from the cell models better identifies MYCN-driven retinoblastoma than MYCN amplification and can identify cases that may benefit from MYCN-targeted therapy. MYCN drives tumor progression in a molecularly defined retinoblastoma subgroup, and inhibiting MYCN activity could restore a more differentiated and less aggressive tumor biology.

Single-shot X-ray phase-contrast imaging is used to take high-resolution images of laser-driven strong shock waves. Employing a two-grating Talbot interferometer, we successfully acquire standard absorption, differential phase-contrast, and dark-field images of the shocked target. Good agreement is demonstrated between experimental data and the results of two-dimensional radiation hydrodynamics simulations of the laser–plasma interaction. The main sources of image noise are identified through a thorough assessment of the interferometer’s performance. The acquired images demonstrate that grating-based phase-contrast imaging is a powerful diagnostic tool for high-energy-density science. In addition, we make a novel attempt at using the dark-field image as a signal modality of Talbot interferometry to identify the microstructure of a foam target.

Principal component analysis (PCA) and kernel PCA allow the decorrelation of data with respect to a basis that is found via variance maximization. However, these techniques are based on pointwise correlations. Especially in the context of time series analysis this is not optimal. We present a novel generalization of PCA that allows to imprint any desired correlation pattern. Thus the proposed method can be used to incorporate previously known statistical dependencies between input variables into the model which is increasing the overall performance. This is achieved by generalizing the projection onto the direction of maximum variance—as known from PCA—to a projection onto a multi-dimensional subspace. We focus on the use of cyclic correlation patterns, which is especially of interest in the domain of time series analysis. Beneath introducing the presented variation of PCA, we discuss the role of this method with respect to other well-known time series analysis techniques.

Granulocyte-colony stimulating factor (GCSF) is a widely used therapeutic protein to treat neutropenia. GCSF has an increased propensity to aggregate if the pH is increased above 5.0. Although GCSF is very well experimentally characterized, the exact pH-dependent aggregation mechanism of GCSF is still under debate. This study aimed to model the complex pH-dependent aggregation behavior of GCSF using state-of-the-art simulation techniques. The conformational stability of GCSF was investigated by performing metadynamics simulations, while the protein-protein interactions were investigated using coarse-grained (CG) simulations of multiple GCSF monomers. The CG simulations were directly compared with small-angle X-ray (SAXS) data. The metadynamics simulations demonstrated that the orientations of Trp residues in GCSF are dependent on pH. The conformational change of Trp residues is due to the loss of Trp-His interactions at the physiological pH, which in turn may increase protein flexibility. The helical structure of GCSF was not affected by the pH conditions of the simulations. Our CG simulations indicate that at pH 4.0, the colloidal stability may be more important than the conformational stability of GCSF. The electrostatic potential surface and CG simulations suggested that the basic residues are mainly responsible for colloidal stability as deprotonation of these residues causes a reduction of the highly positively charged electrostatic barrier close to the aggregation-prone long loop regions.

Computational methods play a key role for investigating allosteric mechanisms in proteins, with the potential of generating valuable insights for innovative drug design. Here we present the SenseNet (“Structure ENSEmble NETworks”) framework for analysis of protein structure networks, which differs from established network models by focusing on interaction timelines obtained by molecular dynamics simulations. This approach is evaluated by predicting allosteric residues reported by NMR experiments in the PDZ2 domain of hPTP1e, a reference system for which previous computational predictions have shown considerable variance. We applied two models based on the mutual information between interaction timelines to estimate the conformational influence of each residue on its local environment. In terms of accuracy our prediction model is comparable to the top performing model published for this system, but by contrast benefits from its independence from NMR structures. Our results are complementary to experimental data and the consensus of previous predictions, demonstrating the potential of our new analysis tool SenseNet. Biochemical interpretation of our model suggests that allosteric residues in the PDZ2 domain form two distinct clusters of contiguous sidechain surfaces. SenseNet is provided as a plugin for the network analysis software Cytoscape, allowing for ease of future application and contributing to a system of compatible tools bridging the fields of system and structural biology.

Ceramides are lipids that act directly on mitochondria to trigger apoptosis, but the underlying mechanism remains largely unclear. Here authors use a photoactivatable ceramide probe combined with a computation approach and functional studies to identify the voltage-dependent anion channel VDAC2 as a direct effector of ceramide-mediated cell death.

The multi-domain protein UHRF1 is essential for DNA methylation maintenance and binds DNA via a base-flipping mechanism with a preference for hemi-methylated CpG sites. We investigated its binding to hemi- and symmetrically modified DNA containing either 5-methylcytosine (mC), 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), or 5-carboxylcytosine (caC). Our experimental results indicate that UHRF1 binds symmetrically carboxylated and hybrid methylated/carboxylated CpG dyads in addition to its previously reported substrates. Complementary molecular dynamics simulations provide a possible mechanistic explanation of how the protein could differentiate between modification patterns. First, we observe different local binding modes in the nucleotide binding pocket as well as the protein's NKR finger. Second, both DNA modification sites are coupled through key residues within the NKR finger, suggesting a communication pathway affecting protein-DNA binding for carboxylcytosine modifications. Our results suggest a possible additional function of the hemi-methylation reader UHRF1 through binding of carboxylated CpG sites. This opens the possibility of new biological roles of UHRF1 beyond DNA methylation maintenance and of oxidised methylcytosine derivates in epigenetic regulation.

Abstract Background Plant cytosolic NAD-dependent glyceraldehyde-3-phosphate dehydrogenase (GapC) displays redox-dependent changes in its subcellular localizations and activity. Apart from its fundamental role in glycolysis, it also exhibits moonlighting properties. Since the exceptional redox-sensitivity of GapC has been suggested to play a crucial role in its various functions, we here studied its redox-dependent subcellular localization and the influence of the redox-state on GapC protein interactions. Results In mesophyll protoplasts from Arabidopsis thaliana, colocalization of GapC with mitochondria was more pronounced under reducing conditions than upon oxidative stress. In accordance, reduced GapC showed an increased affinity to the mitochondrial voltage-dependent anion-selective channel (VDAC) compared to the oxidized one. On the other hand, nuclear localization of GapC was increased under oxidizing conditions. The essential role of the catalytic cysteine for nuclear translocation was shown by using the corresponding cysteine mutants. Furthermore, interaction of GapC with the thioredoxin Trx-h3 as a candidate to revert the redox-modifications, occurred in the nucleus of oxidized protoplasts. In a yeast complementation assay, we could demonstrate that the plant-specific non-phosphorylating glyceraldehyde 3-P dehydrogenase (GapN) can substitute for glucose 6-P dehydrogenase to generate NADPH for re-reduction of the Trx system and ROS defense. Conclusions The preferred association of reduced, glycolytically active GapC with VDAC suggests a substrate-channeling metabolon at the mitochondrial surface for efficient energy generation. Increased occurrence of oxidized GapC in the nucleus points to a function in signal transduction and gene expression. Furthermore, the interaction of GapC with Trx-h3 in the nucleus indicates reversal of the oxidative cysteine modification after re-establishment of cellular homeostasis. Both, energy metabolism and signal transfer for long-term adjustment and protection from redox-imbalances are mediated by the various functions of GapC. The molecular properties of GapC as a redox-switch are key to its multiple roles in orchestrating energy metabolism.

Abstract Data on intratumoral heterogeneity of small intestine neuroendocrine tumors (SI-NETs) and related liver metastasis are limited. The aim of this study was to characterize genetic heterogeneity of 5 patients with SI-NETs. Therefore, formalin-fixed, paraffin-embedded tissue samples of primary and metastatic lesions as well as benign liver of five patients with synchronously metastasized, well differentiated SI-NETs were analyzed with whole exome sequencing. For one patient, chip based 850k whole DNA methylome analysis was performed of primary and metastatic tumor tissue as well as control tissue. Thereby, 156 single nucleotide variants (SNVs) in 150 genes were identified and amount of mutations per sample ranged from 9–34 (mean 22). The degree of common (0–94%) and private mutations per sample was strongly varying (6–100%). In all patients, copy number variations (CNV) were found and the degree of intratumoral heterogeneity of CNVs corresponded to SNV analysis. DNA methylation analysis of a patient without common SNVs revealed a large overlap of common methylated CpG sites. In conclusion, SI-NET primary and metastatic lesions show a highly varying degree of intratumoral heterogeneity. Driver events might not be detectable with exome analysis only, and further comprehensive studies including whole genome and epigenetic analyses are warranted.

Background and study aims Endoscopic retrograde cholangiopancreatography (ERCP) and/or extracorporeal shock wave lithotripsy are first-line therapies for draining an obstructed pancreatic duct (PD) in painful chronic calcifying pancreatitis (CCP). Pancreaticoscopy has shown promising success rates in small series. Materials and methods This study was a retrospective analysis of a clinical database. Included were all digital single-operator digital video (SOV) pancreaticoscopy-guided interventions (n = 23) on CCP patients (n = 20) between 2015 and 2017. Success and complication rates were collected from the database. Clinical success was determined by assessing pain level score (NRS) and quality of life (QoL) using standardized questionnaires. Results Overall technical success rate (successful SOV-pancreaticoscopy and PD drainage) was 95 %. Adverse events occurred in 7 of 23 procedures (30 %) and included extravasation from the PD (n = 1), self-limiting post-sphincterotomy bleeding (n = 1) and post-ERCP pancreatitis (PEP) (n = 6). At 3- to 6-month follow-up, 95 % of patients reported improvement in symptoms and reduction in intake of analgesics. Mean NRS decreased from 5.4 (±1.6) to 2.8 (± 1.8) (P

In this paper, we investigated the behavior of a type II superconducting armature when accelerated by a pulsed magnetic field generated by a single-stage pancake coil. While conducting this investigation, we performed a numerical finite element simulation and an experimental study of the magnetic field dynamics at the edge of the pancake coil when the payload was a superconducting disc made from YBa2Cu3O7−x, cooled down to 77 K. The magnetic field measurements were performed using a CMR-B-scalar sensor, which was able to measure the absolute magnitude of the magnetic field and was specifically manufactured in order to increase the sensor’s sensitivity up to 500 mT. It was obtained that type II superconducting armatures can outperform normal metals when the launch conditions are tailored to their electromagnetic properties.

DNA methylation was shown previously to be a crucial mechanism responsible for transcriptional deregulation in the pathogenesis of classical Hodgkin lymphoma (cHL). To identify epigenetically inactivated miRNAs in cHL, we have analyzed the set of miRNAs downregulated in cHL cell lines using bisulfite pyrosequencing. We focused on miRNAs with promoter regions located within or IL15 and HOMER1 transcripts as well as between mir-148a-5p and SUB1 and SERPINH1 transcripts. Furthermore, mir-148a overexpression resulted in reduced cell proliferation in the KM-H2 cell line. In summary, we report that mir-148a is a novel tumor suppressor inactivated in cHL and that epigenetic silencing of miRNAs is a common phenomenon in cHL.

Background: The selective sodium-glucose cotransporter 2 (SGLT-2) inhibitor empagliflozin leads to improved cardiovascular, renal and heart failure outcome in secondary prevention. To better understand these effects, we examined vascular function and central hemodynamics. Methods: In this prospective, double-blind, randomized, placebo-controlled, crossover study 76 patients with untreated type 2 diabetes were randomized to empagliflozin 25 mg orally once daily or placebo. After 6 weeks of treatment with either empagliflozin or placebo and 1 week wash-out-phase, patients crossed over to the other treatment. Central hemodynamics and vascular function were assessed by central systolic blood pressure (BP), central pulse pressure, forward and backward wave amplitude under office (Sphygmocor, AtCor, Australia) as well as ambulatory conditions (Mobilograph, IEM, Aachen). Results: Treatment with empagliflozin reduced central systolic BP (114 ± 12 vs. 119 ± 14 mmHg, p < 0.001), central diastolic BP (74.4 ± 6.9 vs. 76.8 ± 8.2 mmHg, p = 0.004) and central pulse pressure (39.5 ± 9.9 vs. 42.2 ± 11 mmHg, p = 0.012) compared to placebo. Forward (p = 0.006) and backward (p = 0.026) reflection amplitude, assessed under office conditions, were also significantly lower with empagliflozin than with placebo. Under ambulatory conditions over 24-hours we also observed lower central systolic (117 ± 9 vs. 119 ± 9 mmHg, p = 0.059) and diastolic (79 ± 7 vs. 81 ± 7 mmHg, p = 0.011) BP after 6 weeks treatment with empagliflozin compared to placebo. Pulse wave velocity under ambulatory conditions was also reduced after 6 weeks with empagliflozin (p = 0.016). Conclusions: Our study demonstrated consistent significant improvements of vascular function and central hemodynamics with empagliflozin under office and ambulatory conditions. Our data support the concept that empagliflozin exerts beneficial effects on cardiovascular and heart failure outcome via improved vascular function.

P2X4 and P2X7 are members of the P2X receptor family, comprising seven isoforms (P2X1–P2X7) that form homo- and heterotrimeric non-specific cation channels gated by extracellular ATP. P2X4 and P2X7 are widely coexpressed, particularly in secretory epithelial cells and immune and inflammatory cells, and regulate inflammation and nociception. Although functional heteromerization has been established for P2X2 and P2X3 subunits expressed in sensory neurons, there are contradictory reports regarding a functional interaction between P2X4 and P2X7 subunits. To resolve this issue, we coexpressed P2X4 and P2X7 receptor subunits labeled with green (EGFP) and red (TagRFP) fluorescent proteins in Xenopus laevis oocytes and investigated a putative physical interaction between the fusion proteins by Förster resonance energy transfer (FRET). Coexpression of P2X4 and P2X7 subunits with EGFP and TagRFP located in the extracellular receptor domains led to significant FRET signals. Significant FRET signals were also measured between C-terminally fluorophore-labeled full-length P2X41-384 and C-terminally truncated fluorescent P2X71-408 subunits. We furthermore used the two-electrode voltage clamp technique to investigate whether human P2X4 and P2X7 receptors (hP2X4, hP2X7) functionally interact at the level of ATP-induced whole-cell currents. Concentration–response curves and effects of ivermectin (P2X4-potentiating drug) or BzATP (P2X7-specific agonist) were consistent with a model in which coexpressed hP2X4 and hP2X7 do not interact. Similarly, the effect of adding specific inhibitors of P2X4 (PSB-15417) or P2X7 (oATP, A438079) could be explained by a model in which only homomers exist, and that these are blocked by the respective antagonist. In conclusion, we show that P2X4 and P2X7 subunits can form heterotrimeric P2X4/P2X7 receptors. However, unlike observations for P2X2 and P2X3, coexpression of P2X4 and P2X7 subunits does not result in a novel electrophysiologically discriminable P2X receptor phenotype.

A new single-axis gas thermal gyroscope without proof mass is presented in this paper. The device was designed, manufactured and experimentally characterized. The obtained results were compared to numerical simulation. The working principle of the gyroscope is based on the deflection of a laminar gas flow caused by the Coriolis effect. A bidirectional hot air flow is generated by alternating activation of two suspended resistive micro-heaters. The heated gas is encapsulated in a semi-open cavity and the gas expands primarily inside the cavity. The thermal expansion gyroscope has a simple structure. Indeed, the device is composed of a micromachined cavity on which three bridges are suspended. The central bridge is electrically separated into two segments enabling to set up two heaters which may be supplied independently from each other. The two other bridges, placed symmetrically on each side of the central bridge, are equipped with temperature detectors which measure variations in gas temperature. The differential temperature depends on the rotational velocity applied to the system. Various parameters such as the heating duty cycle, the type of the gas and the power injected into the heaters have been studied to define the optimal working conditions required to obtain the highest level of sensitivity over a measurement range of around 1000°/s. The robustness of the device has also been tested and validated for a shock resistance of 10,000 g for a duration of 400 µs.

We investigated the mechanism of how the papillomavirus E2 transcription factor can activate promoters through activator protein (AP)1 binding sites. Using an unbiased approach with an inducible cell line expressing the viral transcription factor E2 and transcriptome analysis, we found that E2 induces the expression of the two AP1 components c-Fos and FosB in a Brd4-dependent manner. In vitro RNA interference confirmed that c-Fos is one of the AP1 members driving the expression of viral oncogenes E6/E7. Mutation analysis and in vivo RNA interference identified an essential role for c-Fos/AP1 and also for the bromodomain protein Brd4 for papillomavirus-induced tumorigenesis. Lastly, chromatin immunoprecipitation analysis demonstrated that E2 binds together with Brd4 to a canonical E2 binding site (E2BS) in the promoter of c-Fos, thus activating c-Fos expression. Thus, we identified a novel way how E2 activates the viral oncogene promoter and show that E2 may act as a viral oncogene by direct activation of c-Fos involved in skin tumorigenesis.

The bristle sensillum of the imago of Drosophila is made of four cells that arise from a sensory organ precursor cell (SOP). This SOP is selected within proneural clusters (PNC) through a mechanism that involves Notch signalling. PNCs are defined through the expression domains of the proneural genes, whose activities enables cells to become SOPs. They encode tissue specific bHLH proteins that form functional heterodimers with the bHLH protein Daughterless (Da). In the prevailing lateral inhibition model for SOP selection, a transcriptional feedback loop that involves the Notch pathway amplifies small differences of proneural activity between cells of the PNC. As a result only one or two cells accumulate sufficient proneural activity to adopt the SOP fate. Most of the experiments that sustained the prevailing lateral inhibition model were performed a decade ago. We here re-examined the selection process using recently available reagents. Our data suggest a different picture of SOP selection. They indicate that a band-like region of proneural activity exists. In this proneural band the activity of the Notch pathway is required in combination with Emc to define the PNCs. We found a sub-group in the PNCs from which a pre-selected SOP arises. Our data indicate that most imaginal disc cells are able to adopt a proneural state from which they can progress to become SOPs. They further show that bristle formation can occur in the absence of the proneural genes if the function of emc is abolished. These results suggest that the tissue specific proneural proteins of Drosophila have a similar function as in the vertebrates, which is to determine the time of emergence and position of the SOP and to stabilise the proneural state.