Microscope-integrated optical coherence tomography for in vivo human brain tumor detection with artificial intelligence

OBJECTIVE

It has been shown that optical coherence tomography (OCT) can identify brain tumor tissue and potentially be used for intraoperative margin diagnostics. However, there is limited evidence on its use in human in vivo settings, particularly in terms of its applicability and accuracy of residual brain tumor detection (RTD). For this reason, a microscope-integrated OCT system was examined to determine in vivo feasibility of RTD after resection with automated scan analysis.

METHODS

Healthy and diseased brain was 3D scanned at the resection edge in 18 brain tumor patients and investigated for its informative value in regard to intraoperative tissue classification. Biopsies were taken at these locations and labeled by a neuropathologist for further analysis as ground truth. Optical OCT properties were obtained, compared, and used for separation with machine learning. In addition, two artificial intelligence-assisted methods were utilized for scan classification, and all approaches were examined for RTD accuracy and compared to standard techniques.

RESULTS

In vivo OCT tissue scanning was feasible and easily integrable into the surgical workflow. Measured backscattered light signal intensity, signal attenuation, and signal homogeneity were significantly distinctive in the comparison of scanned white matter to increasing levels of scanned tumor infiltration (p < 0.001) and achieved high values of accuracy (85%) for the detection of diseased brain in the tumor margin with support vector machine separation. A neuronal network approach achieved 82% accuracy and an autoencoder approach 85% accuracy in the detection of diseased brain in the tumor margin. Differentiating cortical gray matter from tumor tissue was not technically feasible in vivo.

CONCLUSIONS

In vivo OCT scanning of the human brain has been shown to contain significant value for intraoperative RTD, supporting what has previously been discussed for ex vivo OCT brain tumor scanning, with the perspective of complementing current intraoperative methods for this purpose, especially when deciding to withdraw from further resection toward the end of the surgery.

Feeding strategies for Sporosarcina pasteurii cultivation unlock more efficient production of ureolytic biomass for MICP

The bacterium Sporosarcina pasteurii is the most commonly used microorganism for Microbial Induced Calcite Precipitation (MICP) due to its high urease activity. To date, no proper fed-batch cultivation protocol for S. pasteurii has been published, even though this cultivation method has a high potential for reducing costs of producing microbial ureolytic biomass. This study focusses on fed-batch cultivation of S. pasteurii DSM33. The study distinguishes between limited fed-batch cultivation and extended batch cultivation. Simply feeding glucose to a S. pasteurii culture does not seem beneficial. However, it was exploited that S. pasteurii is auxotrophic for two vitamins and amino acids. Limited fed-batch cultivation was accomplished by feeding the necessary vitamins or amino acids to a culture lacking them. Feeding nicotinic acid to a nicotinic acid deprived culture resulted in a 24% increase of the specific urease activity compared to a fed culture without nicotinic acid limitation. Also, extended batch cultivation was explored. Feeding a mixture of glucose and yeast extract results in OD600 of ≈70 at the end of cultivation, which is the highest value published in literature so far. These results have the potential to make MICP applications economically viable.

Contrast enhanced endoscopic ultrasound detects early therapy response following anti-TNF-therapy in patients with ulcerative colitis

BACKGROUND AND AIM

Though colonoscopy plays a crucial role in assessing active ulcerative colitis (aUC), its scope is limited to the mucosal surface. Endoscopic ultrasound (EUS) coupled with contrast-enhancement (dCEUS) can precisely quantify bowel wall thickness and microvascular circulation, potentially enabling the quantitative evaluation of inflammation.We conducted a prospective, longitudinal study to assess therapy response using dCEUS in aUC patients undergoing treatment with adalimumab (ADA) or infliximab (IFX).

METHODS

30 ADA- and 15 IFX-treated aUC patients were examined at baseline and at 2, 6, 14 weeks of therapy and 48 weeks of follow-up. Bowel wall thickness (BWT) was measured by EUS in the rectum. Vascularity was quantified by dCEUS using Rise Time (RT) and Time To Peak (TTP). Therapy response was defined after 14 weeks using the Mayo Score.

RESULTS

Patients with aUC displayed a mean BWT of 3.9±0.9 mm. In case of response to ADA/IFX a significant reduction in BWT was observed after 2 weeks (p=0.04), whereas non-responders displayed no significant changes. The TTP was notably accelerated at baseline and significantly normalised by week 2 in responders (p=0.001), while non-responders exhibited no significant alterations (p=0.9). At week 2, the endoscopic Mayo score did not exhibit any changes, thus failing to predict treatment responses.

CONCLUSION

dCEUS enables the early detection of therapy response in patients with aUC, which serves as a predictive marker for long term clinical success. Therefore, dCEUS serves as a diagnostic tool for assessing the probability of future therapy success.

High-resolution rectoscopy using MHz optical coherence tomography: a step towards real time 3D endoscopy

Colonoscopy and endoscopic ultrasound play pivotal roles in the assessment of rectal diseases, especially rectal cancer and inflammatory bowel diseases. Optical coherence tomography (OCT) offers a superior depth resolution, which is a critical factor for individualizing the therapeutic concept and evaluating the therapy response. We developed two distinct rectoscope prototypes, which were integrated into a 1300 nm MHz-OCT system constructed at our facility. The rapid rotation of the distal scanning probe at 40,000 revolutions per minute facilitates a 667 Hz OCT frame rate, enabling real-time endoscopic imaging of large areas. The performance of these OCT-rectoscopes was assessed in an ex vivo porcine colon and a post mortem human in-situ colon. The OCT-rectoscope consistently distinguished various layers of the intestinal wall, identified gut-associated lymphatic tissue, and visualized a rectal polyp during the imaging procedure with 3D-reconstruction in real time. Subsequent histological examination confirmed these findings. The body donor was preserved using an ethanol-glycerol-lysoformin-based technique for true-to-life tissue consistency. We could demonstrate that the novel MHZ-OCT-rectoscope effectively discriminates rectal wall layers and crucial tissue characteristics in a post mortem human colon in-situ. This real-time-3D-OCT holds promise as a valuable future diagnostic tool for assessing disease state and therapy response on-site in rectal diseases.

Mechanical characteristics of glioblastoma and peritumoral tumor-free human brain tissue

BACKGROUND

The diagnosis of brain tumor is a serious event for the affected patient. Surgical resection is a crucial part in the treatment of brain tumors. However, the distinction between tumor and brain tissue can be difficult, even for experienced neurosurgeons. This is especially true in the case of gliomas. In this project we examined whether the biomechanical parameters elasticity and stress relaxation behavior are suitable as additional differentiation criteria between tumorous (glioblastoma multiforme; glioblastoma, IDH-wildtype; GBM) and non-tumorous, peritumoral tissue.

METHODS

Indentation measurements were used to examine non-tumorous human brain tissue and GBM samples for the biomechanical properties of elasticity and stress-relaxation behavior. The results of these measurements were then used in a classification algorithm (Logistic Regression) to distinguish between tumor and non-tumor.

RESULTS

Differences could be found in elasticity spread and relaxation behavior between tumorous and non-tumorous tissue. Classification was successful with a sensitivity/recall of 83% (sd = 12%) and a precision of 85% (sd = 9%) for detecting tumorous tissue.

CONCLUSION

The findings imply that the data on mechanical characteristics, with particular attention to stress relaxation behavior, can serve as an extra element in differentiating tumorous brain tissue from non-tumorous brain tissue.

Squalene production under oxygen limitation by Schizochytrium sp. S31 in different cultivation systems

The triterpene squalene is widely used in the food, cosmetics and pharmaceutical industries due to its antioxidant, antistatic and anti-carcinogenic properties. It is usually obtained from the liver of deep sea sharks, which are facing extinction. Alternative production organisms are marine protists from the family Thraustochytriaceae, which produce and store large quantities of various lipids. Squalene accumulation in thraustochytrids is complex, as it is an intermediate in sterol biosynthesis. Its conversion to squalene 2,3-epoxide is the first step in sterol synthesis and is heavily oxygen dependent. Hence, the oxygen supply during cultivation was investigated in our study. In shake flask cultivations, a reduced oxygen supply led to increased squalene and decreased sterol contents and yields. Oxygen-limited conditions were applied to bioreactor scale, where squalene accumulation and growth of Schizochytrium sp. S31 was determined in batch, fed-batch and continuous cultivation. The highest dry matter (32.03 g/L) was obtained during fed-batch cultivation, whereas batch cultivation yielded the highest biomass productivity (0.2 g/L*h-1). Squalene accumulation benefited from keeping the microorganisms in the growth phase. Therefore, the highest squalene content of 39.67 ± 1.34 mg/g was achieved by continuous cultivation (D = 0.025 h-1) and the highest squalene yield of 1131 mg/L during fed-batch cultivation. Volumetric and specific squalene productivity both reached maxima in the continuous cultivation at D = 0.025 h-1 (6.94 ± 0.27 mg/L*h-1 and 1.00 ± 0.03 mg/g*h-1, respectively). Thus, the choice of a suitable cultivation method under oxygen-limiting conditions depends heavily on the process requirements. KEY POINTS: • Measurements of respiratory activity and backscatter light of thraustochytrids • Oxygen limitation increased squalene accumulation in Schizochytrium sp. S31 • Comparison of different cultivation methods under oxygen-limiting conditions.

Virtual Hall sensor triggered multi-MHz endoscopic OCT imaging for stable real-time visualization

Circumferential scanning in endoscopic imaging is crucial across various disciplines, and optical coherence tomography (OCT) is often the preferred choice due to its high-speed, high-resolution, and micron-scale imaging capabilities. Moreover, real-time and high-speed 3D endoscopy is a pivotal technology for medical screening and precise surgical guidance, among other applications. However, challenges such as image jitter and non-uniform rotational distortion (NURD) are persistent obstacles that hinder real-time visualization during high-speed OCT procedures. To address this issue, we developed an innovative, low-cost endoscope that employs a brushless DC motor for scanning, and a sensorless technique for triggering and synchronizing OCT imaging with the scanning motor. This sensorless approach uses the motor's electrical feedback (back electromotive force, BEMF) as a virtual Hall sensor to initiate OCT image acquisition and synchronize it with a Fourier Domain Mode-Locked (FDML)-based Megahertz OCT system. Notably, the implementation of BEMF-triggered OCT has led to a substantial reduction in image jitter and NURD (<4 mrad), thereby opening up a new window for real-time visualization capabilities. This approach suggests potential benefits across various applications, aiming to provide a more accurate, deployable, and cost-effective solution. Subsequent studies can explore the adaptability of this system to specific clinical scenarios and its performance under practical endoscopic conditions.

Phase unwrapping for MHz optical coherence elastography and application to brain tumor tissue

During neuro-oncologic surgery, phase-sensitive optical coherence elastography (OCE) can be valuable for distinguishing between healthy and diseased tissue. However, the phase unwrapping process required to retrieve the original phase signal is a challenging and critical task. To address this issue, we demonstrate a one-dimensional unwrapping algorithm that recovers the phase signal from a 3.2 MHz OCE system. With a processing time of approximately 0.11 s per frame on the GPU, multiple 2π wraps are detected and corrected. By utilizing this approach, exact and reproducible information on tissue deformation can be obtained with pixel accuracy over the entire acquisition time. Measurements of brain tumor-mimicking phantoms and human ex vivo brain tumor samples verified the algorithm's reliability. The tissue samples were subjected to a 200 ms short air pulse. A correlation with histological findings confirmed the algorithm's dependability.

828 kHz retinal imaging with an 840 nm Fourier domain mode locked laser

This paper presents a Fourier domain mode locked (FDML) laser centered around 840 nm. It features a bidirectional sweep repetition rate of 828 kHz and a spectral bandwidth of 40 nm. An axial resolution of ∼9.9 µm in water and a 1.4 cm sensitivity roll-off are achieved. Utilizing a complex master-slave (CMS) recalibration method and due to a sufficiently high sensitivity of 84.6 dB, retinal layers of the human eye in-vivo can be resolved during optical coherence tomography (OCT) examination. The developed FDML laser enables acquisition rates of 3D-volumes with a size of 200 × 100 × 256 voxels in under 100 milliseconds. Detailed information on the FDML implementation, its challenging design tasks, and OCT images obtained with the laser are presented in this paper.

Sclerosing Mesenteritis

A patient with light chain multiple myeloma and no evidence of disease following autologous bone marrow transplantation, developed asymptomatic mass in the right lower quadrant mesentery, which increased in size and showed FDG uptake on PET CT. The only other change of note on imaging was chronic appendicitis, confirmed on surgery and pathology. Suspecting a neoplastic mass in the mesentery, surgical resection was undertaken but the pathology revealed sclerosing mesenteritis. This rare, non-neoplastic fibro-inflammatory disease, its protean manifestations, disease associations, and treatment are briefly discussed, including the perplexing coexistence with adjacent appendicitis.

Hemophagocytic lymphohistiocytosis-like hyperinflammation due to a de novo mutation in DPP9

BACKGROUND

Genetic defects in components of inflammasomes can cause autoinflammation. Biallelic loss-of-function mutations in dipeptidyl peptidase 9 (DPP9), a negative regulator of the NLRP1 and CARD8 inflammasomes, have recently been shown to cause an inborn error of immunity characterized by pancytopenia, skin manifestations, and increased susceptibility to infections.

OBJECTIVE

We sought to study the molecular basis of autoinflammation in a patient with severe infancy-onset hyperinflammation associated with signs of fulminant hemophagocytic lymphohistiocytosis.

METHODS

Using heterologous cell models as well as patient cells, we performed genetic, immunologic, and molecular investigations to identify the genetic cause and to assess the impact of the identified mutation on inflammasome activation.

RESULTS

The patient exhibited pancytopenia with decreased neutrophils and T, B, and natural killer cells, and markedly elevated levels of lactate dehydrogenase, ferritin, soluble IL-2 receptor, and triglycerides. In addition, serum levels of IL-1β and IL-18 were massively increased, consistent with inflammasome activation. Genetic analysis revealed a previously undescribed de novo mutation in DPP9 (c.755G>C, p.Arg252Pro) affecting a highly conserved amino acid residue. The mutation led to destabilization of the DPP9 protein as shown in transiently transfected HEK293T cells and in patient-derived induced pluripotent stem cells. Using functional inflammasome assays in HEK293T cells, we demonstrated that mutant DPP9 failed to restrain the NLRP1 and CARD8 inflammasomes, resulting in constitutive inflammasome activation. These findings suggest that the Arg252Pro DPP9 mutation acts in a dominant-negative manner.

CONCLUSIONS

A de novo mutation in DPP9 leads to severe infancy-onset autoinflammation because of unleashed inflammasome activation.

When a smile is still a conflict: Affective conflicts from emotional facial expressions of ingroup or outgroup members occur irrespective of the social interaction context

Facial expressions play a crucial role in human interactions. Typically, a positive (negative) expression evokes a congruent positive (negative) reaction within the observer. This congruent behavior is inverted, however, when the same positive (negative) expression is displayed by an outgroup member. Two approaches provide an explanation for this phenomenon. The social intentions account proposes underlying social messages within the facial display, whereas the processing conflict account assumes an affective conflict triggered by incongruent combinations of emotion and the affective connotation of group membership. In three experiments, we aimed at further substantiating the processing conflict account by separating the affective conflict from potential social intentions. For this, we created a new paradigm, in which the participant was an outside observer of a social interaction scene between two faces. Participants were required to respond to the emotional target person that could represent an ingroup or outgroup member. In all three experiments, irrespective of any social intention, responses were consistently affected by the group relation between participant and emotional target, i.e., the affective (in)congruency of the target seen by participants. These results further support the processing conflict account. The implications for the two theoretical accounts are discussed.

Four-wave mixing seeded by a rapid wavelength-sweeping FDML laser for nonlinear imaging at 900 nm and 1300 nm

Four-wave mixing (FWM) enables the generation and amplification of light in spectral regions where suitable fiber gain media are unavailable. The 1300 nm and 900 nm regions are of especially high interest for time-encoded (TICO) stimulated Raman scattering microscopy and spectro-temporal laser imaging by diffracted excitation (SLIDE) two-photon microscopy. We present a new, to the best of our knowledge, FWM setup where we shift the power of a home-built fully fiber-based master oscillator power amplifier (MOPA) at 1064 nm to the 1300-nm region of a rapidly wavelength-sweeping Fourier domain mode-locked (FDML) laser in a photonic crystal fiber (PCF) creating pulses in the 900-nm region. The resulting 900-nm light can be wavelength swept over 54 nm and has up to 2.5 kW (0.2 µJ) peak power and a narrow instantaneous spectral linewidth of 70 pm. The arbitrary pulse patterns of the MOPA and the fast wavelength tuning of the FDML laser (419 kHz) allow it to rapidly tune the FWM light enabling new and faster TICO-Raman microscopy, SLIDE imaging, and other applications.

PANGAEA - Data Publisher for Earth & Environmental Science

The information system PANGAEA provides targeted support for research data management as well as long-term data archiving and publication. PANGAEA is operated as an open access library for archiving, publishing, and distributing georeferenced data from earth and environmental sciences. It focuses on observational and experimental data. Citability, comprehensive metadata descriptions, interoperability of data and metadata, a high degree of structural and semantic harmonization of the data inventory as well as the commitment of the hosting institutions ensures the long-term usability of archived data. PANGAEA is a pioneer of FAIR and open data infrastructures to enable data intensive science and an integral component of national and international science and technology activities. This paper provides an overview of the recent organisational, structural, and technological advancements in developing and operating the information system.

Build-up and dephasing of Floquet-Bloch bands on subcycle timescales

Strong light fields have created opportunities to tailor novel functionalities of solids1-5. Floquet-Bloch states can form under periodic driving of electrons and enable exotic quantum phases6-15. On subcycle timescales, lightwaves can simultaneously drive intraband currents16-29 and interband transitions18,19,30,31, which enable high-harmonic generation16,18,19,21,22,25,28-30 and pave the way towards ultrafast electronics. Yet, the interplay of intraband and interband excitations and their relation to Floquet physics have been key open questions as dynamical aspects of Floquet states have remained elusive. Here we provide this link by visualizing the ultrafast build-up of Floquet-Bloch bands with time-resolved and angle-resolved photoemission spectroscopy. We drive surface states on a topological insulator32,33 with mid-infrared fields-strong enough for high-harmonic generation-and directly monitor the transient band structure with subcycle time resolution. Starting with strong intraband currents, we observe how Floquet sidebands emerge within a single optical cycle; intraband acceleration simultaneously proceeds in multiple sidebands until high-energy electrons scatter into bulk states and dissipation destroys the Floquet bands. Quantum non-equilibrium calculations explain the simultaneous occurrence of Floquet states with intraband and interband dynamics. Our joint experiment and theory study provides a direct time-domain view of Floquet physics and explores the fundamental frontiers of ultrafast band-structure engineering.

Ultrafast Spectral Tuning of a Fiber Laser for Time-Encoded Multiplex Coherent Raman Scattering Microscopy

Coherent Raman scattering microscopy utilizing bioorthogonal tagging approaches like isotope or alkyne labeling allows for a targeted monitoring of spatial distribution and dynamics of small molecules of interest in cells, tissues, and other complex biological matrices. To fully exploit this approach in terms of real-time monitoring of several Raman tags, e.g., to study drug uptake dynamics, extremely fast tunable lasers are needed. Here, we present a laser concept without moving parts and fully electronically controlled for the quasi-simultaneous acquisition of coherent anti-Stokes Raman scattering images at multiple Raman resonances. The laser concept is based on the combination of a low noise and spectrally narrow Fourier domain mode-locked laser seeding a compact four wave mixing-based high-power fiber-based optical parametric amplifier.

The neurosurgical benefit of contactless in vivo optical coherence tomography regarding residual tumor detection: A clinical study

Purpose

In brain tumor surgery, it is crucial to achieve complete tumor resection while conserving adjacent noncancerous brain tissue. Several groups have demonstrated that optical coherence tomography (OCT) has the potential of identifying tumorous brain tissue. However, there is little evidence on human in vivo application of this technology, especially regarding applicability and accuracy of residual tumor detection (RTD). In this study, we execute a systematic analysis of a microscope integrated OCT-system for this purpose.

Experimental design

Multiple 3-dimensional in vivo OCT-scans were taken at protocol-defined sites at the resection edge in 21 brain tumor patients. The system was evaluated for its intraoperative applicability. Tissue biopsies were obtained at these locations, labeled by a neuropathologist and used as ground truth for further analysis. OCT-scans were visually assessed with a qualitative classifier, optical OCT-properties were obtained and two artificial intelligence (AI)-assisted methods were used for automated scan classification. All approaches were investigated for accuracy of RTD and compared to common techniques.

Results

Visual OCT-scan classification correlated well with histopathological findings. Classification with measured OCT image-properties achieved a balanced accuracy of 85%. A neuronal network approach for scan feature recognition achieved 82% and an auto-encoder approach 85% balanced accuracy. Overall applicability showed need for improvement.

Conclusion

Contactless in vivo OCT scanning has shown to achieve high values of accuracy for RTD, supporting what has well been described for ex vivo OCT brain tumor scanning, complementing current intraoperative techniques and even exceeding them in accuracy, while not yet in applicability.

Chemoproteomics-Enabled Identification of 4-Oxo-β-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9

Dipeptidyl peptidases 8 and 9 (DPP8/9) have gathered interest as drug targets due to their important roles in biological processes like immunity and tumorigenesis. Elucidation of their distinct individual functions remains an ongoing task and could benefit from the availability of novel, chemically diverse and selective chemical tools. Here, we report the activity-based protein profiling (ABPP)-mediated discovery of 4-oxo-β-lactams as potent, non-substrate-like nanomolar DPP8/9 inhibitors. X-ray crystallographic structures revealed different ligand binding modes for DPP8 and DPP9, including an unprecedented targeting of an extended S2' (eS2') subsite in DPP8. Biological assays confirmed inhibition at both target and cellular levels. Altogether, our integrated chemical proteomics and structure-guided small molecule design approach led to novel DPP8/9 inhibitors with alternative molecular inhibition mechanisms, delivering the highest selectivity index reported to date.

Dipeptidyl peptidase 9 triggers BRCA2 degradation and promotes DNA damage repair

N-terminal sequences are important sites for post-translational modifications that alter protein localization, activity, and stability. Dipeptidyl peptidase 9 (DPP9) is a serine aminopeptidase with the rare ability to cleave off N-terminal dipeptides with imino acid proline in the second position. Here, we identify the tumor-suppressor BRCA2 as a DPP9 substrate and show this interaction to be induced by DNA damage. We present crystallographic structures documenting intracrystalline enzymatic activity of DPP9, with the N-terminal Met1-Pro2 of a BRCA21-40 peptide captured in its active site. Intriguingly, DPP9-depleted cells are hypersensitive to genotoxic agents and are impaired in the repair of DNA double-strand breaks by homologous recombination. Mechanistically, DPP9 targets BRCA2 for degradation and promotes the formation of RAD51 foci, the downstream function of BRCA2. N-terminal truncation mutants of BRCA2 that mimic a DPP9 product phenocopy reduced BRCA2 stability and rescue RAD51 foci formation in DPP9-deficient cells. Taken together, we present DPP9 as a regulator of BRCA2 stability and propose that by fine-tuning the cellular concentrations of BRCA2, DPP9 alters the BRCA2 interactome, providing a possible explanation for DPP9's role in cancer.

Intravascular optical coherence elastography

Optical coherence elastography (OCE), a functional extension of optical coherence tomography (OCT), visualizes tissue strain to deduce the tissue's biomechanical properties. In this study, we demonstrate intravascular OCE using a 1.1 mm motorized catheter and a 1.6 MHz Fourier domain mode-locked OCT system. We induced an intraluminal pressure change by varying the infusion rate from the proximal end of the catheter. We analysed the pixel-matched phase change between two different frames to yield the radial strain. Imaging experiments were carried out in a phantom and in human coronary arteries in vitro. At an imaging speed of 3019 frames/s, we were able to capture the dynamic strain. Stiff inclusions in the phantom and calcification in atherosclerotic plaques are associated with low strain values and can be distinguished from the surrounding soft material, which exhibits elevated strain. For the first time, circumferential intravascular OCE images are provided side by side with conventional OCT images, simultaneously mapping both the tissue structure and stiffness.

Case report: Optical coherence tomography for monitoring biologic therapy in psoriasis and atopic dermatitis

Biologic therapies are increasingly used to treat chronic inflammatory skin diseases such as psoriasis and atopic dermatitis. In clinical practice, scores based on evaluation of objective and subjective symptoms are used to assess disease severity, leading to evaluation of treatment goals with clinical decisions on treatment initiation, switch to another treatment modality or to discontinue current treatment. However, this visual-based scoring is relatively subjective and inaccurate due to inter- and intraobserver reliability. Optical coherence tomography (OCT) is a fast, high-resolution, in vivo imaging modality that enables the visualization of skin structure and vasculature. We evaluated the use of OCT for quantification and monitoring of skin inflammation to improve objective assessment of disease activity in patients with psoriasis and atopic dermatitis. We assessed the following imaging parameters including epidermal thickness, vascular density, plexus depth, vessel diameter, and vessel count. A total of four patients with psoriasis or atopic dermatitis were treated with biologic agents according to current treatment guidelines. OCT was used to monitor their individual treatment response in a target lesion representing disease activity for 52 weeks. Psoriatic and eczema lesions exhibited higher epidermal thickness, increased vascular density, and higher vessel count compared to uninvolved skin. An upward shift of the superficial vascular plexus accompanied by smaller vessel diameters was seen in psoriasis in contrast to atopic dermatitis, where larger vessels were observed. A response to biologic therapy was characterized by normalization of the imaging parameters in the target lesions in comparison to uninvolved skin during the observation period of 52 weeks. Optical coherence tomography potentially serves as an instrument to monitor biologic therapy in inflammatory skin diseases. Imaging parameters may enable objective quantification of inflammation in psoriasis or atopic dermatitis in selected representative skin areas. OCT may reveal persistent subclinical inflammation in atopic dermatitis beyond clinical remission.

Developing a fluorometric urease activity microplate assay suitable for automated microbioreactor experiments

Quantifying urease activity is an important task for Microbial Induced Calcite Precipitation research. A new urease activity microplate assay using a fluorescent pH indicator is presented. The method is also suitable for automated measurements during microbioreactor experiments. The assay reagent consists of the green fluorescent pH-indicator fluorescein, urea and a phosphate buffer. After sample addition, the microbial urease hydrolyses urea, which results in a pH and hence fluorescence increase. The fluorescence signal can be measured with a microplate reader or with the microbioreactor system BioLector, allowing for automated urease activity measurements during cultivation experiments. In both measurement systems, the fluorescence signal slope highly correlates with the urease activity measured offline with standard methods. Automated measurement is possible, as no sample preparation such as centrifugation or adjusting of the optical density is required. The assay was developed so that the culture samples turbidity, salinity or buffer concentration does not have a negative impact on the fluorescence signal. The assay allows for straightforward, non-hazardous, parallelized, cheap and reliable measurements, making research on ureolytic bacteria for Microbial Induced Calcite Precipitation more efficient. The assay could be adapted to other enzymes, which have a strong impact on the pH value.

Differentiation of different stages of brain tumor infiltration using optical coherence tomography: Comparison of two systems and histology

The discrimination of tumor-infiltrated tissue from non-tumorous brain tissue during neurosurgical tumor excision is a major challenge in neurosurgery. It is critical to achieve full tumor removal since it directly correlates with the survival rate of the patient. Optical coherence tomography (OCT) might be an additional imaging method in the field of neurosurgery that enables the classification of different levels of tumor infiltration and non-tumorous tissue. This work investigated two OCT systems with different imaging wavelengths (930 nm/1310 nm) and different resolutions (axial (air): 4.9 μm/16 μm, lateral: 5.2 μm/22 μm) in their ability to identify different levels of tumor infiltration based on freshly excised ex vivo brain samples. A convolutional neural network was used for the classification. For both systems, the neural network could achieve classification accuracies above 91% for discriminating between healthy white matter and highly tumor infiltrated white matter (tumor infiltration >60%) .This work shows that both OCT systems with different optical properties achieve similar results regarding the identification of different stages of brain tumor infiltration.

Printed temperature sensor array for high-resolution thermal mapping

Fully-printed temperature sensor arrays—based on a flexible substrate and featuring a high spatial-temperature resolution—are immensely advantageous across a host of disciplines. These range from healthcare, quality and environmental monitoring to emerging technologies, such as artificial skins in soft robotics. Other noteworthy applications extend to the fields of power electronics and microelectronics, particularly thermal management for multi-core processor chips. However, the scope of temperature sensors is currently hindered by costly and complex manufacturing processes. Meanwhile, printed versions are rife with challenges pertaining to array size and sensor density. In this paper, we present a passive matrix sensor design consisting of two separate silver electrodes that sandwich one layer of sensing material, composed of poly(3,4-ethylenedioxythiophene):polystyrene sulfonate (PEDOT:PSS). This results in appreciably high sensor densities of 100 sensor pixels per cm$$^2$$ 2 for spatial-temperature readings, while a small array size is maintained. Thus, a major impediment to the expansive application of these sensors is efficiently resolved. To realize fast and accurate interpretation of the sensor data, a neural network (NN) is trained and employed for temperature predictions. This successfully accounts for potential crosstalk between adjacent sensors. The spatial-temperature resolution is investigated with a specially-printed silver micro-heater structure. Ultimately, a fairly high spatial temperature prediction accuracy of 1.22  °C is attained.

Fabrication of Bragg Mirrors by Multilayer Inkjet Printing

Bragg mirrors are widely applied in optical and photonic devices due to their capability of light management. However, the fabrication of Bragg mirrors is mainly accomplished by physical and chemical vapor deposition processes, which are costly and do not allow for lateral patterning. Here, the fabrication of Bragg mirrors by fully inkjet printing is reported. The photonic bandgap of Bragg mirrors is tailored by adjusting the number of bilayers in the stack and the layer thickness via simply varying printing parameters. An ultrahigh reflectance of 99% is achieved with the devices consisting of ten bilayers only, and the central wavelength of Bragg mirrors is tuned from visible into near-infrared wavelength range. Inkjet printing allows for fabricating Bragg mirrors on various substrates (e.g., glass and foils), in different sizes and variable lateral patterns. The printed Bragg mirrors not only exhibit a high reflection at designed wavelengths but also show an outstanding homogeneity in color over a large area. The approach thus enables additive manufacturing for various applications ranging from microscale photonic elements to enhanced functionality and aesthetics in large-area displays and solar technologies.

Registration of histological brain images onto optical coherence tomography images based on shape information

Identifying tumour infiltration zones during tumour resection in order to excise as much tumour tissue as possible without damaging healthy brain tissue is still a major challenge in neurosurgery. The detection of tumour infiltrated regions so far requires histological analysis of biopsies taken from at expected tumour boundaries. The gold standard for histological analysis is the staining of thin cut specimen and the evaluation by a neuropathologist. This work presents a way to transfer the histological evaluation of a neuropathologist onto optical coherence tomography (OCT) images. OCT is a method suitable for real timein vivoimaging during neurosurgery however the images require processing for the tumour detection. The method demonstrated here enables the creation of a dataset which will be used for supervised learning in order to provide a better visualization of tumour infiltrated areas for the neurosurgeon. The created dataset contains labelled OCT images from two different OCT-systems (wavelength of 930 nm and 1300 nm). OCT images corresponding to the stained histological images were determined by shaping the sample, a controlled cutting process and a rigid transformation process between the OCT volumes based on their topological information. The histological labels were transferred onto the corresponding OCT images through a non-rigid transformation based on shape context features retrieved from the sample outline in the histological image and the OCT image. The accuracy of the registration was determined to be 200 ± 120μm. The resulting dataset consists of 1248 labelled OCT images for each of the two OCT systems.

Intersubband Polariton-Polariton Scattering in a Dispersive Microcavity

The ultrafast scattering dynamics of intersubband polaritons in dispersive cavities embedding GaAs/AlGaAs quantum wells are studied directly within their band structure using a noncollinear pump-probe geometry with phase-stable midinfrared pulses. Selective excitation of the lower polariton at a frequency of ∼25  THz and at a finite in-plane momentum k_{‖} leads to the emergence of a narrowband maximum in the probe reflectivity at k_{‖}=0. A quantum mechanical model identifies the underlying microscopic process as stimulated coherent polariton-polariton scattering. These results mark an important milestone toward quantum control and bosonic lasing in custom-tailored polaritonic systems in the mid and far infrared.

Erratum: Spectroscopic thermo-elastic optical coherence tomography for tissue characterization: publisher's note

[This corrects the article on p. 1430 in vol. 13, PMID: 35414978.].

Spectroscopic thermo-elastic optical coherence tomography for tissue characterization

Optical imaging techniques that provide free space, label free imaging are powerful tools in obtaining structural and biochemical information in biological samples. To date, most of the optical imaging technologies create images with a specific contrast and require multimodality integration to add additional contrast. In this study, we demonstrate spectroscopic Thermo-elastic Optical Coherence Tomography (TE-OCT) as a potential tool in tissue identification. TE-OCT creates images based on two different forms of contrast: optical reflectance and thermo-elastic deformation. TE-OCT uses short laser pulses to induce thermo-elastic tissue deformation and measures the resulting surface displacement using phase-sensitive OCT. In this work we characterized the relation between thermo-elastic displacement and optical absorption, excitation, fluence and illumination area. The experimental results were validated with a 2-dimensional analytical model. Using spectroscopic TE-OCT, the thermo-elastic spectra of elastic phantoms and tissue components in coronary arteries were extracted. Specific tissue components, particularly lipid, an important biomarker for identifying atherosclerotic lesions, can be identified in the TE-OCT spectral response. As a label-free, free-space, dual-contrast, all-optical imaging technique, spectroscopic TE-OCT holds promise for biomedical research and clinical pathology diagnosis.

Continuous spectral zooming for in vivo live 4D-OCT with MHz A-scan rates and long coherence

We present continuous three-dimensional spectral zooming in live 4D-OCT using a home-built FDML based OCT system with 3.28 MHz A-scan rate. Improved coherence characteristics of the FDML laser allow for imaging ranges up to 10 cm. For the axial spectral zoom feature, we switch between high resolution and long imaging range by adjusting the sweep range of our laser. We present a new imaging setup allowing for synchronized adjustments of the imaging range and lateral field of view during live OCT imaging. For this, a novel inline recalibration algorithm was implemented that enables numerical k-linearization of the raw OCT fringes for every frame instead of every volume. This is realized by acquiring recalibration data within the dead time of the raster scan at the turning points of the fast axis scanner. We demonstrate in vivo OCT images of fingers and hands at different resolution modes and show real three-dimensional zooming during live 4D-OCT. A three-dimensional spectral zooming feature for live 4D-OCT is expected to be a useful tool for a wide range of biomedical, scientific and research applications, especially in OCT guided surgery.

Field-resolved high-order sub-cycle nonlinearities in a terahertz semiconductor laser

The exploitation of ultrafast electron dynamics in quantum cascade lasers (QCLs) holds enormous potential for intense, compact mode-locked terahertz (THz) sources, squeezed THz light, frequency mixers, and comb-based metrology systems. Yet the important sub-cycle dynamics have been notoriously difficult to access in operational THz QCLs. Here, we employ high-field THz pulses to perform the first ultrafast two-dimensional spectroscopy of a free-running THz QCL. Strong incoherent and coherent nonlinearities up to eight-wave mixing are detected below and above the laser threshold. These data not only reveal extremely short gain recovery times of 2 ps at the laser threshold, they also reflect the nonlinear polarization dynamics of the QCL laser transition for the first time, where we quantify the corresponding dephasing times between 0.9 and 1.5 ps with increasing bias currents. A density-matrix approach reproducing the emergence of all nonlinearities and their ultrafast evolution, simultaneously, allows us to map the coherently induced trajectory of the Bloch vector. The observed high-order multi-wave mixing nonlinearities benefit from resonant enhancement in the absence of absorption losses and bear potential for a number of future applications, ranging from efficient intracavity frequency conversion, mode proliferation to passive mode locking.

From Alpha Diversity to Zzz: Interactions among sleep, the brain, and gut microbiota in the first year of life

Sleep disorders have been linked to alterations of gut microbiota composition in adult humans and animal models, but it is unclear how this link develops. With longitudinal assessments in 162 healthy infants, we present a so far unrecognized sleep-brain-gut interrelationship. First, we report a link between sleep habits and gut microbiota: daytime sleep is associated with bacterial diversity, and nighttime sleep fragmentation and variability link with bacterial maturity and enterotype. Second, we demonstrate a sleep-brain-gut link: bacterial diversity and enterotype are associated with sleep neurophysiology. Third, we show that the sleep-brain-gut link is relevant in development: sleep habits and bacterial markers predict behavioral-developmental outcomes. Our results demonstrate the dynamic interplay between sleep, gut microbiota, and the maturation of brain and behavior during infancy, which aligns with the lately emerging concept of a sleep-brain-gut axis. Importantly, sleep and gut microbiota represent promising health targets since both can be modified non-invasively. As many adult diseases root in early childhood, leveraging protective factors of adequate sleep and age-appropriate gut microbiota in infancy could constitute a health promoting factor across the entire human lifespan.

An automated solution for measuring the progress toward FAIR research data

With a rising number of scientific datasets published and the need to test their Findable, Accessible, Interoperable, and Reusable (FAIR) compliance repeatedly, data stakeholders have recognized the importance of an automated FAIR assessment. This paper presents a programmatic solution for assessing the FAIRness of research data. We describe the translation of the FAIR data principles into measurable metrics and the application of the metrics in evaluating FAIR compliance of research data through an open-source tool we developed. For each metric, we conceptualized and implemented practical tests drawn upon prevailing data curation and sharing practices, and the paper discusses their rationales. We demonstrate the work by evaluating multidisciplinary datasets from trustworthy repositories, followed by recommendations and improvements. We believe our experience in developing and applying the metrics in practice and the lessons we learned from it will provide helpful information to others developing similar approaches to assess different types of digital objects and services.

Apixaban for treatment of embolic stroke of undetermined source (ATTICUS) randomized trial – update of patient characteristics and study timeline after interim analysis

Background

Secondary prevention after embolic stroke of undetermined source (ESUS) has not yet been established. ESUS is associated with high risk of recurrent ischemic stroke and clinically silent ischemic lesions. Secondary prevention with aspirin is the current standard therapy in ESUS patients, despite high prevalence of occult atrial fibrillation (AF).

Purpose

To determine whether the direct oral factor Xa inhibitor apixaban, started within 28 days after index stroke, is superior to aspirin in preventing new ischemic lesions in subjects with remote cardiac monitoring. Primary endpoint was detection of new ischemic lesions in flair and diffusion-weighted (DWI) MR imaging at 12 months follow-up.

Methods

The study enrolled ESUS patients with risk profile for cardiac thromboembolism (i.e., left atrium (LA) size &gt;45 mm, spontaneous echo contrast in LA appendage, LA appendage flow velocity ≤0.2 cm/s, atrial high rate episodes, CHA2DS2-Vasc score ≥4, patent foramen ovale). Patients were randomized 1:1 into the aspirin and apixaban arms. Study drug was initiated within 3–28 days after minor/moderate stroke and 14–28 days after major stroke. MRI (Flair/DWI) was conducted within 7 days of AF detection by remote cardiac monitors and at 12 months. ClinicalTrials.gov Identifier: NCT02427126. Funding: The trial is supported by BMS-Pfizer Alliance.

Results

Enrollment was stopped after interims analysis (including 200 patients) due to futility. Overall, 373 patients were screened with 353 being enrolled (178 and 175 in apixaban and ASA arms, respectively). So far, 130 (73.0%) and 120 (68.6%) subjects from apixaban and ASA arms, respectively, completed the study. 2% death, 1.7% withdrawal, and 1.7% were lost to follow-up. 3.9% did not completed the study for other reasons. Mean age of the ATTICUS population was 68.5 years with 51% males. 80% of the subjects suffered from hypertension. Mean systolic blood pressure at enrollment was 132 mmHg, BMI was 27.7, and CHA2DS-VASc-Score was 4.9. So far, adverse events (AE) occurred in 63% of the subjects, 30% was documented as severe. 6.8% cases of recurrent ischemic stroke and no case of hemorrhagic stroke were reported. Only 1 case of severe bleeding was reported in the aspirin arm. Newly detected AF was reported in 80 patients (23%), 42 occurring in the aspirin arm. As required by protocol, latter were immediately switched from aspirin to apixaban. Due to ongoing data clearing, numbers and % will change until presentation.

Conclusions

In contrast to the recently published NAVIGATE and RESPECT ESUS trials, patients enrolled in ATTICUS need to exhibit additional AF predicting factors. Furthermore, mandatory cardiac remote monitoring will help to elucidate the impact of AF and the effects of early oral anticoagulation with apixaban compared to antiplatelet therapy with aspirin on the incidence of new ischemic lesions after ESUS. Preliminary data will be presented and discussed in the context of current literature.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): The trial is supported by BMS-Pfizer Alliance.

Microscopic optical coherence tomography (mOCT) at 600 kHz for 4D volumetric imaging and dynamic contrast

Volumetric imaging of dynamic processes with microscopic resolution holds a huge potential in biomedical research and clinical diagnosis. Using supercontinuum light sources and high numerical aperture (NA) objectives, optical coherence tomography (OCT) achieves microscopic resolution and is well suited for imaging cellular and subcellular structures of biological tissues. Currently, the imaging speed of microscopic OCT (mOCT) is limited by the line-scan rate of the spectrometer camera and ranges from 30 to 250 kHz. This is not fast enough for volumetric imaging of dynamic processes in vivo and limits endoscopic application. Using a novel CMOS camera, we demonstrate fast 3-dimensional OCT imaging with 600,000 A-scans/s at 1.8 µm axial and 1.1 µm lateral resolution. The improved speed is used for imaging of ciliary motion and particle transport in ex vivo mouse trachea. Furthermore, we demonstrate dynamic contrast OCT by evaluating the recorded volumes rather than en face planes or B-scans. High-speed volumetric mOCT will enable the correction of global tissue motion and is a prerequisite for applying dynamic contrast mOCT in vivo. With further increase in imaging speed and integration in flexible endoscopes, volumetric mOCT may be used to complement or partly replace biopsies.

Time-encoded stimulated Raman scattering microscopy of tumorous human pharynx tissue in the fingerprint region from 1500-1800 cm-1

Stimulated Raman scattering (SRS) microscopy for biomedical analysis can provide a molecular localization map to infer pathological tissue changes. Compared to spontaneous Raman, SRS achieves much faster imaging speeds at reduced spectral coverage. By targeting spectral features in the information dense fingerprint region, SRS allows fast and reliable imaging. We present time-encoded (TICO) SRS microscopy of unstained head-and-neck biopsies in the fingerprint region with molecular contrast. We combine a Fourier-domain mode-locked (FDML) laser with a master oscillator power amplifier (MOPA) to cover Raman transitions from 1500-1800cm^-1. Both lasers are fiber-based and electronically programmable making this fingerprint TICO system robust and reliable. The results of our TICO approach were cross-checked with a spontaneous Raman micro-spectrometer and show good agreement, paving the way toward clinical applications.

Rest Is Required to Learn an Appetitively-Reinforced Operant Task in Drosophila

Maladaptive operant conditioning contributes to development of neuropsychiatric disorders. Candidate genes have been identified that contribute to this maladaptive plasticity, but the neural basis of operant conditioning in genetic model organisms remains poorly understood. The fruit fly Drosophila melanogaster is a versatile genetic model organism that readily forms operant associations with punishment stimuli. However, operant conditioning with a food reward has not been demonstrated in flies, limiting the types of neural circuits that can be studied. Here we present the first sucrose-reinforced operant conditioning paradigm for flies. In the paradigm, flies walk along a Y-shaped track with reward locations at the terminus of each hallway. When flies turn in the reinforced direction at the center of the track, they receive a sucrose reward at the end of the hallway. Only flies that rest early in training learn the reward contingency normally. Flies rewarded independently of their behavior do not form a learned association but have the same amount of rest as trained flies, showing that rest is not driven by learning. Optogenetically-induced sleep does not promote learning, indicating that sleep itself is not sufficient for learning the operant task. We validated the sensitivity of this assay to detect the effect of genetic manipulations by testing the classic learning mutant dunce. Dunce flies are learning-impaired in the Y-Track task, indicating a likely role for cAMP in the operant coincidence detector. This novel training paradigm will provide valuable insight into the molecular mechanisms of disease and the link between sleep and learning.