Selective gene expression profiling contributes to a better understanding of the molecular pathways underlying the histological changes observed after RHMVL

Background

In previous studies, five vasoactive drugs were investigated for their effect on the recovery process after extended liver resection without observing relevant improvements. We hypothesized that an analysis of gene expression could help to identify potentially druggable pathways and could support the selection of promising drug candidates.

Methods

Liver samples obtained from rats after combined 70% partial hepatectomy and right median hepatic vein ligation (n = 6/group) sacrificed at 0 h, 24 h, 48 h, and 7days were selected for this study. Liver samples were collected from differentially perfused regions of the median lobe (obstruction-zone, border-zone, normal-zone). Gene expression profiling of marker genes regulating hepatic hemodynamics, vascular remodeling, and liver regeneration was performed with microfluidic chips. We used 3 technical replicates from each sample. Raw data were normalized using LEMming and differentially expressed genes were identified using LIMMA.

Results

The strongest differences were found in obstruction-zone at 24 h and 48 h postoperatively compared to all other groups. mRNA expression of marker genes from hepatic hemodynamics pathways (iNOS,Ptgs2,Edn1) was most upregulated.

Conclusion

These upregulated genes suggest a strong vasoconstrictive effect promoting arterial hypoperfusion in the obstruction-zone. Reducing iNOS expression using selective iNOS inhibitors seems to be a promising approach to promote vasodilation and liver regeneration.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01364-z.

Semantic Segmentation of Intralobular and Extralobular Tissue from Liver Scaffold H&E Images

Decellularized tissue is an important source for biological tissue engineering. Evaluation of the quality of decellularized tissue is performed using scanned images of hematoxylin-eosin stained (H&E) tissue sections and is usually dependent on the observer. The first step in creating a tool for the assessment of the quality of the liver scaffold without observer bias is the automatic segmentation of the whole slide image into three classes: the background, intralobular area, and extralobular area. Such segmentation enables to perform the texture analysis in the intralobular area of the liver scaffold, which is crucial part in the recellularization procedure. Existing semi-automatic methods for general segmentation (i.e., thresholding, watershed, etc.) do not meet the quality requirements. Moreover, there are no methods available to solve this task automatically. Given the low amount of training data, we proposed a two-stage method. The first stage is based on classification of simple hand-crafted descriptors of the pixels and their neighborhoods. This method is trained on partially annotated data. Its outputs are used for training of the second-stage approach, which is based on a convolutional neural network (CNN). Our architecture inspired by U-Net reaches very promising results, despite a very low amount of the training data. We provide qualitative and quantitative data for both stages. With the best training setup, we reach 90.70% recognition accuracy.

Novel morphological multi-scale evaluation system for quality assessment of decellularized liver scaffolds

Decellularized scaffolds can serve as an excellent three-dimensional environment for cell repopulation. They maintain tissue-specific microarchitecture of extracellular matrix proteins with important spatial cues for cell adhesion, migration, growth, and differentiation. However, criteria for quality assessment of the three-dimensional structure of decellularized scaffolds are rather fragmented, usually study-specific, and mostly semi-quantitative. Thus, we aimed to develop a robust structural assessment system for decellularized porcine liver scaffolds. Five scaffolds of different quality were used to establish the new evaluation system. We combined conventional semi-quantitative scoring criteria with a quantitative scaffold evaluation based on automated image analysis. For the quantitation, we developed a specific open source software tool (ScaffAn) applying algorithms designed for texture analysis, segmentation, and skeletonization. ScaffAn calculates selected parameters characterizing structural features of porcine liver scaffolds such as the sinusoidal network. After evaluating individual scaffolds, the total scores predicted scaffold interaction with cells in terms of cell adhesion. Higher scores corresponded to higher numbers of cells attached to the scaffolds. Moreover, our analysis revealed that the conventional system could not identify fine differences between good quality scaffolds while the additional use of ScaffAn allowed discrimination. This led us to the conclusion that only using the combined score resulted in the best discrimination between different quality scaffolds. Overall, our newly defined evaluation system has the potential to select the liver scaffolds most suitable for recellularization, and can represent a step toward better success in liver tissue engineering.

Modulation of hepatic perfusion did not improve recovery from hepatic outflow obstruction

Background

Focal hepatic venous outflow obstruction frequently occurs after extended liver resection and leads to a portal hypertension, arterial hypoperfusion and parenchymal necrosis.

In this study, we investigated the pharmacological modulation of liver perfusion and hepatic damage in a surgical model of hepatic outflow obstruction after extended liver resection by administration of 5 different drugs in comparison to an operative intervention, splenectomy.

Methods

Male inbred Lewis rats (Lew/Crl) were subjected to right median hepatic vein ligation + 70% partial hepatectomy. Treatment consisted of a splenectomy or the application of saline, carvedilol or isosorbide-5-mononitrate (ISMN) (5 mg · kg⁻¹ respectively 7,2 mg · kg⁻¹ per gavage 12 h⁻¹). The splenectomy was performed during operation. The effect of the treatments on hepatic hemodynamics were measured in non-operated animals, immediately after operation (n = 4/group) and 24 h after operation (n = 5/group). Assessment of hepatic damage (liver enzymes, histology) and liver cell proliferation (BrdU-immunohistochemistry) was performed 24 h after operation. Furthermore sildenafil (10 μg · kg⁻¹ i.p. 12h⁻¹), terlipressin (0.05 mg · kg⁻¹ i.v. 12 h⁻¹) and octreotide (10 μg · kg⁻¹ s.c. 12 h⁻¹) were investigated regarding their effect on hepatic hemodynamics and hepatic damage 24 h after operation (n = 4/group).

Results

Carvedilol and ISMN significantly decreased the portal pressure in normal non-operated rats from 11,1 ± 1,1 mmHg (normal rats) to 8,4 ± 0,3 mmHg (carvedilol) respectively 7,4 ± 1,8 mmHg (ISMN). ISMN substantially reduced surgery-induced portal hypertension from 15,4 ± 4,4 mmHg to 9,6 ± 2,3 mmHg. Only splenectomy reduced the portal flow immediately after operation by approximately 25%. No treatment had an immediate effect on the hepatic arterial perfusion. In all treatment groups, portal flow increased by approximately 3-fold within 24 h after operation, whereas hepatic arterial flow decreased substantially. Neither treatment reduced hepatic damage as assessed 24 h after operation. The distribution of proliferating cells appeared very similar in all drug treated groups and the splenectomy group.

Conclusion

Transient relative reduction of portal pressure did not result in a reduction of hepatic damage. This might be explained by the development of portal hyperperfusion which was accompanied by arterial hypoperfusion.

Electronic supplementary material

The online version of this article (doi:10.1186/s40360-017-0155-4) contains supplementary material, which is available to authorized users.

Improvement of an Atomic Clock using Squeezed Vacuum

Since the pioneering work of Ramsey, atom interferometers are employed for precision metrology, in particular to measure time and to realize the second. In a classical interferometer, an ensemble of atoms is prepared in one of the two input states, whereas the second one is left empty. In this case, the vacuum noise restricts the precision of the interferometer to the standard quantum limit (SQL). Here, we propose and experimentally demonstrate a novel clock configuration that surpasses the SQL by squeezing the vacuum in the empty input state. We create a squeezed vacuum state containing an average of 0.75 atoms to improve the clock sensitivity of 10000 atoms by 2.05_{-0.37}^{+0.34}  dB. The SQL poses a significant limitation for today's microwave fountain clocks, which serve as the main time reference. We evaluate the major technical limitations and challenges for devising a next generation of fountain clocks based on atomic squeezed vacuum.

Fast and accurate identification of fat droplets in histological images

BACKGROUND AND OBJECTIVE

The accurate identification of fat droplets is a prerequisite for the automatic quantification of steatosis in histological images. A major challenge in this regard is the distinction between clustered fat droplets and vessels or tissue cracks.

METHODS

We present a new method for the identification of fat droplets that utilizes adjacency statistics as shape features. Adjacency statistics are simple statistics on neighbor pixels.

RESULTS

The method accurately identified fat droplets with sensitivity and specificity values above 90%. Compared with commonly-used shape features, adjacency statistics greatly improved the sensitivity toward clustered fat droplets by 29% and the specificity by 17%. On a standard personal computer, megapixel images were processed in less than 0.05s.

CONCLUSIONS

The presented method is simple to implement and can provide the basis for the fast and accurate quantification of steatosis.

Filling an emulsion drop with motile bacteria

We have measured the spatial distribution of motile Escherichia coli inside spherical water droplets emulsified in oil. At low cell concentrations, the cell density peaks at the water-oil interface; at increasing concentration, the bulk of each droplet fills up uniformly while the surface peak remains. Simulations and theory show that the bulk density results from a "traffic" of cells leaving the surface layer, increasingly due to cell-cell scattering as the surface coverage rises above ∼10%. Our findings show similarities with the physics of a rarefied gas in a spherical cavity with attractive walls.

Switching of Swimming Modes in Magnetospirillium gryphiswaldense

The microaerophilic magnetotactic bacterium Magnetospirillum gryphiswaldense swims along magnetic field lines using a single flagellum at each cell pole. It is believed that this magnetotactic behavior enables cells to seek optimal oxygen concentration with maximal efficiency. We analyze the trajectories of swimming M. gryphiswaldense cells in external magnetic fields larger than the earth's field, and show that each cell can switch very rapidly (in <0.2 s) between a fast and a slow swimming mode. Close to a glass surface, a variety of trajectories were observed, from straight swimming that systematically deviates from field lines to various helices. A model in which fast (slow) swimming is solely due to the rotation of the trailing (leading) flagellum can account for these observations. We determined the magnetic moment of this bacterium using a to our knowledge new method, and obtained a value of (2.0±0.6) × 10(-16) A · m(2). This value is found to be consistent with parameters emerging from quantitative fitting of trajectories to our model.

[Video-based self-control in surgical teaching. A new tool in a new concept]

BACKGROUND

Image and video-based results and process control are essential tools of a new teaching concept for conveying surgical skills. The new teaching concept integrates approved teaching principles and new media.

METHOD

Every performance of exercises is videotaped and the result photographically recorded. The quality of the process and result becomes accessible for an analysis by the teacher and the student/learner. The learner is instructed to perform a criteria-based self-analysis of the video and image material by themselves.

RESULTS

The new learning concept has so far been successfully applied in seven rounds within the newly designed modular class "Intensivkurs Chirurgische Techniken" (Intensive training of surgical techniques). Result documentation and analysis via digital picture was completed by almost every student. The quality of the results was high. Interestingly the result quality did not correlate with the time needed for the exercise. The training success had a lasting effect.

CONCLUSION

The new and elaborate concept improves the quality of teaching. In the long run resources for patient care should be saved when training students according to this concept prior to performing tasks in the operating theater. These resources should be allocated for further refining innovative teaching concepts.

Practical quantification of necrosis in histological whole-slide images

Since the histological quantification of necrosis is a common task in medical research and practice, we evaluate different image analysis methods for quantifying necrosis in whole-slide images. In a practical usage scenario, we assess the impact of different classification algorithms and feature sets on both accuracy and computation time. We show how a well-chosen combination of multiresolution features and an efficient postprocessing step enables the accurate quantification necrosis in gigapixel images in less than a minute. The results are general enough to be applied to other areas of histological image analysis as well.

Twin matter waves for interferometry beyond the classical limit

Interferometers with atomic ensembles are an integral part of modern precision metrology. However, these interferometers are fundamentally restricted by the shot noise limit, which can only be overcome by creating quantum entanglement among the atoms. We used spin dynamics in Bose-Einstein condensates to create large ensembles of up to 10(4) pair-correlated atoms with an interferometric sensitivity -1.61(-1.1)(+0.98) decibels beyond the shot noise limit. Our proof-of-principle results point the way toward a new generation of atom interferometers.

Extended coherence time on the clock transition of optically trapped rubidium

Optically trapped ensembles are of crucial importance for frequency measurements and quantum memories but generally suffer from strong dephasing due to inhomogeneous density and light shifts. We demonstrate a drastic increase of the coherence time to 21 s on the magnetic field insensitive clock transition of (87)Rb by applying the recently discovered spin self-rephasing [C. Deutsch et al., Phys. Rev. Lett. 105, 020401 (2010)]. This result confirms the general nature of this new mechanism and thus shows its applicability in atom clocks and quantum memories. A systematic investigation of all relevant frequency shifts and noise contributions yields a stability of 2.4×10(-11)τ(-1/2), where τ is the integration time in seconds. Based on a set of technical improvements, the presented frequency standard is predicted to rival the stability of microwave fountain clocks in a potentially much more compact setup.

Time-Multiplexed Laguerre-Gaussian holographic optical tweezers for biological applications

A ferroelectric liquid crystal spatial light modulator is used to generate up to 24 independently controllable traps in a holographic optical tweezers system using time-multiplexed Fresnel zone plates. For use in biological applications, helical zone plates are used to generate Laguerre-Gaussian laser modes. The high speed switching of the ferroelectric device together with recent advances in computer technology enable fast, smooth movement of traps that can be independently controlled in real time. This is demonstrated by the trapping and manipulation of yeast cells and fungal spores.

Routes towards Anderson-like localization of Bose-Einstein condensates in disordered optical lattices

We investigate, both experimentally and theoretically, possible routes towards Anderson-like localization of Bose-Einstein condensates in disordered potentials. The dependence of this quantum interference effect on the nonlinear interactions and the shape of the disorder potential is investigated. Experiments with an optical lattice and a superimposed disordered potential reveal the lack of Anderson localization. A theoretical analysis shows that this absence is due to the large length scale of the disorder potential as well as its screening by the nonlinear interactions. Further analysis shows that incommensurable superlattices should allow for the observation of the crossover from the nonlinear screening regime to the Anderson localized case within realistic experimental parameters.

Single Molecule Fluorescence Imaging and Its Application to the Study of DNA Condensation

Single molecule fluorescence imaging incorporated with optical tweezers and a laminar flow cell has been used to monitor the kinetic process of DNA condensation induced by spermidine. It was found that at least two steps were involved in the condensation process of the hydrodynamically-stretched linear DNA; a lag period followed by a rapid collapse of DNA. The lag time increased with the flow speed and the collapse time remained short within the range of the flow speed studied. The effect of salt concentration on the condensation process was examined, and the results suggest that the longer lag time observed in the higher salt buffer probably results from the displacement of bound cations and rearrangement of spermidine on the DNA. The flow-speed dependence of the lag time suggests that a nucleation event at the free end of the DNA, i.e. formation of a loop, may play a vital role in the kinetic process of condensation.

Moving interference patterns created using the angular Doppler-effect

We use the angular Doppler-effect to obtain stable frequency shifts from below one Hertz to hundreds of Hertz in the optical domain, constituting a control of 1 part in 1014. For the first time, we use these very small frequency shifts to create continuous motion in interference patterns including the scanning of linear fringe patterns and the rotation of the interference pattern formed from a Laguerre-Gaussian beam. This enables controlled lateral and rotational movement of trapped particles.

Creation and manipulation of three-dimensional optically trapped structures

An interferometric pattern between two annular laser beams is used to construct three-dimensional (3D) trapped structures within an optical tweezers setup. In addition to being fully translatable in three dimensions, the trapped structure can be rotated controllably and continuously by introducing a frequency difference between the two laser beams. These interference patterns could play an important role in the creation of extended 3D crystalline structures.

Controlled rotation of optically trapped microscopic particles

We demonstrate controlled rotation of optically trapped objects in a spiral interference pattern. This pattern is generated by interfering an annular shaped laser beam with a reference beam. Objects are trapped in the spiral arms of the pattern. Changing the optical path length causes this pattern, and thus the trapped objects, to rotate. Structures of silica microspheres, microscopic glass rods, and chromosomes are set into rotation at rates in excess of 5 hertz. This technique does not depend on intrinsic properties of the trapped particle and thus offers important applications in optical and biological micromachines.

Is there any relationship between functional dyspepsia and chronic gastritis associated with Helicobacter pylori infection?

BACKGROUND/AIMS

The relationship between functional dyspepsia, H. pylori infection and chronic gastritis is controversial. Our aims were 1) To determine the prevalence of symptoms and the degree of association between symptoms and histopathological findings in different topographical gastric regions in patients with functional dyspepsia and H. pylori infection; 2) To determine the effect of eradication treatment on functional dyspepsia symptoms.

METHODOLOGY

Prospective randomized study. 251 consecutive patients with dyspepsia (141 women and 110 men), mean age 48.08, SD 16.68 (without ulcer, gastric malignancy or reflux esophageal disease as determined by endoscopy), and with H. pylori infection, underwent upper endoscopy accompanied by the obtaining of 6 biopsies (cardia, corpus, antrum) at baseline, 3 and 6 months after treatment (pantoprazole 40 mg, once daily, amoxycillin 100 mg b.i.d., clarithromycine 500 mg b.i.d.). Inflammation, activity, H. pylori presence and other mucosal alterations were evaluated semi-quantitatively according to the Sydney system, before treatment and 6 months following treatment. An interview that was carried out before, and 6 months following the treatment, determined seven symptoms (scored as 0-3); epigastric burning and pressure, pain after meal, nausea, vomiting, bloating and belching, pain on empty stomach and anorexia. 95% confidence intervals were calculated for mean values of the symptoms and histological findings. The association between symptoms and histological findings was determined by the Kendall tau-b (K tau-b). Using the t test on a 5% level of significance we tested the null hypothesis that symptoms and histological findings were independent variables.

RESULTS

The effectiveness of eradication after 3 months was 87.3% and after 6 months 92.0%. Reinfection rate after 6 months was 6.4% and the overall failure of eradication was 1.6%. Significant decline of chronic inflammation, activity and H. pylori was found in cardia, corpus and antrum (P = 0.001). Glandular atrophy was found to be lower in corpus and antrum (P = 0.001), whereas in cardia an increase was found. Intestinal metaplasia remained unchanged in all gastric regions, whereas a higher degree of foveolar hyperplasia was found, which was most pronounced in corpus and antrum (P = 0.01). There was a significant regression of lymphoid follicles in cardia and antrum (P = 0.001). On the first visit, the mean significant association between symptoms and histological findings was higher, with lower variation of K tau values as compared with the visit 6 months after treatment (K tau-b 0.171, SD 0.05, variation coefficient 30.5% vs. K tau-b 0.167, SD 0.07, variation coefficient 41.5%). According to the topographic distribution of gastritis at the time of the first visit, the mean significant association between symptoms and findings was found to be highest in antrum and corpus as opposed to the visit 6 months after treatment, where the values of association were found to be highest for variables from cardia and lowest for those in gastric corpus. After 6 months both the number of patients complaining of symptoms and dyspepsia score were lower (Wilcoxon P = 0.000).

CONCLUSIONS

Advanced morphological changes of gastric mucosa were found to be significantly associated with symptoms of dysmotility. Pain on an empty stomach is predictive of antral inflammation. Cardia showed higher values of mean association with symptoms 6 months after therapy. Eradication treatment results in an improvement of both inflammatory changes and symptoms. In some patients persisting dysmotility symptoms were associated with persistent inflammation in cardia, which was also true for antrum, however to a lesser degree.

Observation of harmonic generation and nonlinear coupling in the collective dynamics of a bose-einstein condensate

We report the observation of harmonic generation and strong nonlinear coupling of two collective modes of a condensed gas of rubidium atoms. Using a modified time averaged orbiting potential trap we changed the trap anisotropy to a value where the frequency of the m = 0 high-lying mode corresponds to twice the frequency of the m = 0 low-lying mode, thus leading to strong nonlinear coupling between these modes. By changing the anisotropy of the trap and exciting the low-lying mode we observed significant frequency shifts of this fundamental mode and also the generation of its second harmonic.

Observation of the scissors mode and evidence for superfluidity of a trapped bose-einstein condensed Gas

We report the observation of the scissors mode of a Bose-Einstein condensed gas of 87Rb atoms in a magnetic trap, which gives direct evidence of superfluidity in this system. The scissors mode of oscillation is excited by a sudden rotation of the anisotropic trapping potential. For a gas above T(c) (normal fluid) we detect the occurrence of oscillations at two frequencies, with the lower frequency corresponding to the rigid body value of the moment of inertia. Well below T(c) the condensate oscillates at a single frequency, without damping, as expected for a superfluid.

Generation of a beam with a dark focus surrounded by regions of higher intensity: the optical bottle beam

A computer-generated hologram is used to form an optical beam with a localized intensity null at its focus. The beam is a superposition of two Laguerre-Gaussian modes that are phased so that they interfere destructively to give a beam focus that is surrounded in all directions by regions of higher intensity. Beams of this kind will have applications in the optical trapping of macroscopic objects or atoms; hence the term optical bottle beam.