Intra-oscillator high harmonic source reaching 100-eV photon energy.

Resonant enhancement inside an optical cavity has been a wide-spread approach to increase efficiency of nonlinear optical conversion processes while reducing the demands on the driving laser power. This concept has been particularly important for high harmonic generation XUV sources, where passive femtosecond enhancement cavities allowed significant increase in repetition rates required for applications in photoelectron spectroscopy, XUV frequency comb spectroscopy, including the recent endeavor of thorium nuclear clock development. In addition to passive cavities, it has been shown that comparable driving conditions can be achieved inside mode-locked thin-disk laser oscillators, offering a simplified single-stage alternative. This approach is less sensitive to losses thanks to the presence of gain inside the cavity and should thus allow higher conversion efficiencies through tolerating higher intensity in the gas target. Here, we show that the intra-oscillator approach can indeed surpass the much more mature technology of passive enhancement cavities in terms of XUV flux, even reaching comparable values to single-pass sources based on chirped-pulse fiber amplifier lasers. Our system operates at 17 MHz repetition rate generating photon energies between 60 eV and 100 eV. Importantly, this covers the highly attractive wavelength for the silicon industry of 13.5 nm at which our source delivers 60 nW of outcoupled average power per harmonic order.

What shapes template-matching performance in cryogenic electron tomography in situ?

The detection of specific biological macromolecules in cryogenic electron tomography data is frequently approached by applying cross-correlation-based 3D template matching. To reduce computational cost and noise, high binning is used to aggregate voxels before template matching. This remains a prevalent practice in both practical applications and methods development. Here, the relation between template size, shape and angular sampling is systematically evaluated to identify ribosomes in a ground-truth annotated data set. It is shown that at the commonly used binning, a detailed subtomogram average, a sphere and a heart emoji result in near-identical performance. These findings indicate that with current template-matching practices macromolecules can only be detected with high precision if their shape and size are sufficiently different from the background. Using theoretical considerations, the experimental results are rationalized and it is discussed why primarily low-frequency information remains at high binning and that template matching fails to be accurate because similarly shaped and sized macromolecules have similar low-frequency spectra. These challenges are discussed and potential enhancements for future template-matching methodologies are proposed.

ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data.

Cellular cryo-electron tomography (cryo-ET) has emerged as a key method to unravel the spatial and structural complexity of cells in their near-native state at unprecedented molecular resolution. To enable quantitative analysis of the complex shapes and morphologies of lipid membranes, the noisy three-dimensional (3D) volumes must be segmented. Despite recent advances, this task often requires considerable user intervention to curate the resulting segmentations. Here, we present ColabSeg, a Python-based tool for processing, visualizing, editing, and fitting membrane segmentations from cryo-ET data for downstream analysis. ColabSeg makes many well-established algorithms for point-cloud processing easily available to the broad community of structural biologists for applications in cryo-ET through its graphical user interface (GUI). We demonstrate the usefulness of the tool with a range of use cases and biological examples. Finally, for a large Mycoplasma pneumoniae dataset of 50 tomograms, we show how ColabSeg enables high-throughput membrane segmentation, which can be used as valuable training data for fully automated convolutional neural network (CNN)-based segmentation.

The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics.

Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model. Here, we investigate protein folding, unfolding, and misfolding of fast-folding proteins by examining different force fields with their recommended water models, i.e., ff14SB with the TIP3P model and ff19SB with the OPC model. To this end, we generated long conventional MD simulations highlighting the perks and pitfalls of these setups. Using Markov state models, we defined kinetically independent conformational substates and emphasized their distinct characteristics, as well as their corresponding state probabilities. Surprisingly, we found substantial differences in thermodynamics and kinetics of protein folding, depending on the combination of the protein force field and water model, originating primarily from the different water models. These results emphasize the importance of carefully choosing the force field and the respective water model as they determine the accuracy of the observed dynamics of folding events. Thus, the findings support the hypothesis that the water model is at least equally important as the force field and hence needs to be considered in future studies investigating protein dynamics and folding in all areas of biophysics.

Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction.

Senescent cells, which accumulate in organisms over time, contribute to age-related tissue decline. Genetic ablation of senescent cells can ameliorate various age-related pathologies, including metabolic dysfunction and decreased physical fitness. While small-molecule drugs that eliminate senescent cells ('senolytics') partially replicate these phenotypes, they require continuous administration. We have developed a senolytic therapy based on chimeric antigen receptor (CAR) T cells targeting the senescence-associated protein urokinase plasminogen activator receptor (uPAR), and we previously showed these can safely eliminate senescent cells in young animals. We now show that uPAR-positive senescent cells accumulate during aging and that they can be safely targeted with senolytic CAR T cells. Treatment with anti-uPAR CAR T cells improves exercise capacity in physiological aging, and it ameliorates metabolic dysfunction (for example, improving glucose tolerance) in aged mice and in mice on a high-fat diet. Importantly, a single administration of these senolytic CAR T cells is sufficient to achieve long-term therapeutic and preventive effects.

Mid-infrared supermirrors with finesse exceeding 400 000.

For trace gas sensing and precision spectroscopy, optical cavities incorporating low-loss mirrors are indispensable for path length and optical intensity enhancement. Optical interference coatings in the visible and near-infrared (NIR) spectral regions have achieved total optical losses below 2 parts per million (ppm), enabling a cavity finesse in excess of 1 million. However, such advancements have been lacking in the mid-infrared (MIR), despite substantial scientific interest. Here, we demonstrate a significant breakthrough in high-performance MIR mirrors, reporting substrate-transferred single-crystal interference coatings capable of cavity finesse values from 200 000 to 400 000 near 4.5 µm, with excess optical losses (scatter and absorption) below 5 ppm. In a first proof-of-concept demonstration, we achieve the lowest noise-equivalent absorption in a linear cavity ring-down spectrometer normalized by cavity length. This substantial improvement in performance will unlock a rich variety of MIR applications for atmospheric transport and environmental sciences, detection of fugitive emissions, process gas monitoring, breath-gas analysis, and verification of biogenic fuels and plastics.

Structural Basis of the Immunological Cross-Reactivity between Kiwi and Birch Pollen.

Allergies related to kiwi consumption have become a growing health concern, with their prevalence on the rise. Many of these allergic reactions are attributed to cross-reactivity, particularly with the major allergen found in birch pollen. This cross-reactivity is associated with proteins belonging to the pathogenesis-related class 10 (PR-10) protein family. In our study, we determined the three-dimensional structures of the two PR-10 proteins in gold and green kiwi fruits, Act c 8 and Act d 8, using nuclear magnetic resonance (NMR) spectroscopy. The structures of both kiwi proteins closely resemble the major birch pollen allergen, Bet v 1, providing a molecular explanation for the observed immunological cross-reactivity between kiwi and birch pollen. Compared to Act d 11, however, a kiwi allergen that shares the same architecture as PR-10 proteins, structural differences are apparent. Moreover, despite both Act c 8 and Act d 8 containing multiple cysteine residues, no disulfide bridges are present within their structures. Instead, all the cysteines are accessible on the protein's surface and exposed to the surrounding solvent, where they are available for reactions with components of the natural food matrix. This structural characteristic sets Act c 8 and Act d 8 apart from other kiwi proteins with a high cysteine content. Furthermore, we demonstrate that pyrogallol, the most abundant phenolic compound found in kiwi, binds into the internal cavities of these two proteins, albeit with low affinity. Our research offers a foundation for further studies aimed at understanding allergic reactions associated with this fruit and exploring how interactions with the natural food matrix might be employed to enhance food safety.

PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.

The electrostatic properties of proteins arise from the number and distribution of polar and charged residues. Electrostatic interactions in proteins play a critical role in numerous processes such as molecular recognition, protein solubility, viscosity, and antibody developability. Thus, characterizing and quantifying electrostatic properties of a protein are prerequisites for understanding these processes. Here, we present PEP-Patch, a tool to visualize and quantify the electrostatic potential on the protein surface in terms of surface patches, denoting separated areas of the surface with a common physical property. We highlight its applicability to elucidate protease substrate specificity and antibody-antigen recognition and predict heparin column retention times of antibodies as an indicator of pharmacokinetics.

Structure and Dynamics Guiding Design of Antibody Therapeutics and Vaccines.

Antibodies and other new antibody-like formats have emerged as one of the most rapidly growing classes of biotherapeutic proteins. Understanding the structural features that drive antibody function and, consequently, their molecular recognition is critical for engineering antibodies. Here, we present the structural architecture of conventional IgG antibodies alongside other formats. We emphasize the importance of considering antibodies as conformational ensembles in solution instead of focusing on single-static structures because their functions and properties are strongly governed by their dynamic nature. Thus, in this review, we provide an overview of the unique structural and dynamic characteristics of antibodies with respect to their antigen recognition, biophysical properties, and effector functions. We highlight the numerous technical advances in antibody structure prediction and design, enabled by the vast number of experimentally determined high-quality structures recorded with cryo-EM, NMR, and X-ray crystallography. Lastly, we assess antibody and vaccine design strategies in the context of structure and dynamics.

Prophylactic and long-lasting efficacy of senolytic CAR T cells against age-related metabolic dysfunction.

Senescent cells accumulate in organisms over time because of tissue damage and impaired immune surveillance and contribute to age-related tissue decline1,2. In agreement, genetic ablation studies reveal that elimination of senescent cells from aged tissues can ameliorate various age-related pathologies, including metabolic dysfunction and decreased physical fitness3-7. While small-molecule drugs capable of eliminating senescent cells (known as 'senolytics') partially replicate these phenotypes, many have undefined mechanisms of action and all require continuous administration to be effective. As an alternative approach, we have developed a cell-based senolytic therapy based on chimeric antigen receptor (CAR) T cells targeting uPAR, a cell-surface protein upregulated on senescent cells, and previously showed these can safely and efficiently eliminate senescent cells in young animals and reverse liver fibrosis8. We now show that uPAR-positive senescent cells accumulate during physiological aging and that they can be safely targeted with senolytic CAR T cells. Treatment with anti uPAR CAR T cells ameliorates metabolic dysfunction by improving glucose tolerance and exercise capacity in physiological aging as well as in a model of metabolic syndrome. Importantly, a single administration of a low dose of these senolytic CAR T cells is sufficient to achieve long-term therapeutic and preventive effects.

Acquired Brain Injury Among Adolescents and Young Adults: A Nationwide Study of Labor Market Attachment.

Purpose Young patients represent a particularly vulnerable group regarding vocational prognosis after an acquired brain injury (ABI). We aimed to investigate how sequelae and rehabilitation needs are associated with vocational prognosis up to 3 years after an ABI in 15-30-year-old patients. Methods An incidence cohort of 285 patients with ABI completed a questionnaire on sequelae and rehabilitation interventions and needs 3 months after the index hospital contact. They were followed-up for up to 3 years with respect to the primary outcome "stable return to education/work (sRTW)", which was defined using a national register of public transfer payments. Data were analyzed using cumulative incidence curves and cause-specific hazard ratios. Results Young individuals reported a high frequency of mainly pain-related (52%) and cognitive sequelae (46%) at 3 months. Motor problems were less frequent (18%), but negatively associated with sRTW within 3 years (adjusted HR 0.57, 95% CI 0.39-0.84). Rehabilitation interventions were received by 28% while 21% reported unmet rehabilitation needs, and both factors were negatively associated with sRTW (adjusted HR 0.66, 95% CI 0.48-0.91 and adjusted HR 0.72, 95% CI 0.51-1.01). Conclusions Young patients frequently experienced sequelae and rehabilitation needs 3 months post ABI, which was negatively associated with long-term labor market attachment. The low rate of sRTW among patients with sequelae and unmet rehabilitation needs indicates an untapped potential for ameliorated vocational and rehabilitating initiatives targeted at young patients.

Powerful 1-µm 1-GHz optical frequency comb.

A self-referenced optical frequency comb is presented based on Kerr-lens mode-locking of ytterbium-doped CALGO. The robust source delivers 3.5 W average power in 44 fs-long pulses at 1 GHz repetition rate. The residual root-mean-square timing jitter of the emitted pulse-train is 146 fs and the residual integrated phase noise of the carrier-envelope offset frequency is 107 mrad, both in a span from 1 Hz to 10 MHz. After stabilization, 2.7 W average power remains for direct application. This work represents the first multi-mode pumped Kerr-lens mode-locked optical frequency comb at gigahertz-level repetition rate.

Vocational/educational prognosis in adolescents and young adults with acquired brain injury: a nationwide cohort study.

OBJECTIVE: To determine prognostic factors for work ability and employment/educational status among young patients referred to outpatient neurorehabilitation clinics after an acquired brain injury. METHODS: A nationwide cohort study of 471 15-30-year-old patients who attended an interdisciplinary clinical assessment and provided questionnaire data at baseline and after one year. The outcomes were the Work Ability Score (WAS, 0-10 (best)) and employment/educational status after one year. Prognostic performance was analyzed using univariable regression and multivariable Ridge regression in a five-fold cross-validated procedure. RESULTS: Preinjury, 86% of the patients were employed, while the percentage had decreased to 55% at baseline and 52% at follow-up. The model, which included clinical measures of function, showed moderate prognostic performance with respect to WAS (R2=0.29) and employment/educational status (area under the curve (AUC)=0.77). Glasgow Outcome Scale Extended (R2=0.15, AUC=0.68) and the cognitive subscale of the Functional Independence Measure (R2=0.09, AUC=0.64), along with fatigue measured with the Multidimensional Fatigue Inventory (R2=0.15, AUC=0.60) were the single predictors with the highest predictive performance. CONCLUSION: Despite generally high scores in motor and cognitive tests, only about half of the patients were employed at baseline and this proportion remained stable. Global disability, cognitive sequelae and fatigue had the highest prognostic performance.

Continuous Monitoring Versus Intermittent Auscultation of Wheezes in Patients Presenting With Acute Respiratory Distress.

BACKGROUND: Auscultation for an extended period of time using a wearable stethoscope enables objective computerized analysis and longitudinal assessment of lung sounds. However, this auscultation method differs from bedside auscultation in that clinicians are not present to optimize the quality of auscultation. No prior studies have compared these two auscultation methods. OBJECTIVE: The aim of this study was to compare intermittent auscultation using a conventional stethoscope with continuous auscultation using a wearable stethoscope for wheeze detection in patients who present with acute respiratory distress. METHODS: Patients presenting to the emergency department with acute respiratory distress were enrolled. The Strados Remote Electronic Stethoscope Platform (RESP™) was used for continuous auscultation, and intermittent auscultation was performed using a U.S. Food and Drug Administration-cleared electronic stethoscope. A recording was made with an electronic stethoscope. Subsequently, continuous recording was made using RESP™, which continued until the patient was admitted or discharged from the emergency department. The number of captured wheezes in each recording was counted and validated by two board-certified physicians. RESULTS: From May 2018 to May 2019, 43 patients were enrolled in the study. Three patients were excluded from analysis due to incomplete audio recording data. The mean length of recording was 62.3 min for continuous auscultation and 0.7 min for intermittent auscultation; 77.5% (31 of 40) of intermittent recordings contained wheezes, in contrast to 85% (34 of 40) of continuous recordings. CONCLUSIONS: Extending the duration of auscultation using a wearable stethoscope in a noisy clinical environment showed comparable performance to standard of care intermittent auscultation in identifying patients who have wheezes.

Efficient high-power sub-50-fs gigahertz repetition rate diode-pumped solid-state laser.

In this article we present a directly diode-pumped high-power Kerr-lens mode-locked Yb:CALGO bulk laser oscillator operating at 1-GHz repetition rate. We report on two laser configurations optimized for either highest average power or shortest pulse duration. In the first configuration optimized for high average power, the oscillator delivers up to 6.9 W of average power, which is the highest average power of any ultrafast laser oscillator operating at gigahertz repetition rate. The 93-fs pulses have a peak power of 64 kW, and the optical-to-optical efficiency amounts to 37%. In the second configuration optimized for short pulse duration, we demonstrate 48-fs pulses at 4.1 W of average power corresponding to a higher peak power of 74 kW with 21% optical-to-optical efficiency. This is the shortest pulse duration and the highest peak power demonstrated by any GHz-class Yb-based laser oscillator. The compact laser setup is directly pumped by a low-cost multimode fiber-coupled laser diode and has a high potential as an economical yet powerful source for various applications.

Efficient XUV-light out-coupling of intra-cavity high harmonics by a coated grazing-incidence plate.

We experimentally demonstrate an efficient and broadband extreme-ultraviolet light (XUV) out-coupling mechanism of intra-cavity generated high harmonics. The mechanism is based on a coated grazing-incidence plate (GIP), which utilizes the enhanced reflectivity of s-polarized light in comparison to p-polarized light for large angles of incidence (AoI). We design and produce a 60°-AoI coated GIP, tailored specifically for the high demands inside a sub-50-fs Kerr-lens mode-locked Yb:YAG thin-disk laser oscillator in which high harmonic generation (HHG) is driven at ∼450 MW peak power and 17 MHz repetition rate. The coated GIP features an XUV out-coupling efficiency of >25% for photon energies ranging from 10 eV to 60 eV while being anti-reflective for the driving laser field. The XUV spectra reach up to 52 eV in argon and 30 eV in xenon. In a single harmonic, we out-couple 1.3 µW of XUV average power at 37 eV in argon and 5.4 µW at 25 eV in xenon. The combination of an improved HHG driving laser performance and the out-coupling via the coated GIP enabled us to increase the out-coupled XUV average power in a single harmonic by a factor of 20 compared to previous HHG inside ultrafast laser oscillators. Our source approaches the state-of-the-art out-coupled XUV power levels per harmonic of femtosecond enhancement cavities operating at comparable photon energies.

ATG7 is a haploinsufficient repressor of tumor progression and promoter of metastasis.

The role of autophagy in cancer is complex. Both tumor-promoting and tumor-suppressive effects are reported, with tumor type, stage and specific genetic lesions dictating the role. This calls for analysis in models that best recapitulate each tumor type, from initiation to metastatic disease, to specifically understand the contribution of autophagy in each context. Here, we report the effects of deleting the essential autophagy gene Atg7 in a model of pancreatic ductal adenocarcinoma (PDAC), in which mutant KrasG12D and mutant Trp53172H are induced in adult tissue leading to metastatic PDAC. This revealed that Atg7 loss in the presence of KrasG12D/+ and Trp53172H/+ was tumor promoting, similar to previous observations in tumors driven by embryonic KrasG12D/+ and deletion of Trp53. However, Atg7 hemizygosity also enhanced tumor initiation and progression, even though this did not ablate autophagy. Moreover, despite this enhanced progression, fewer Atg7 hemizygous mice had metastases compared with animals wild type for this allele, indicating that ATG7 is a promoter of metastasis. We show, in addition, that Atg7+/- tumors have comparatively lower levels of succinate, and that cells derived from Atg7+/- tumors are also less invasive than those from Atg7+/+ tumors. This effect on invasion can be rescued by ectopic expression of Atg7 in Atg7+/- cells, without affecting the autophagic capacity of the cells, or by treatment with a cell-permeable analog of succinate. These findings therefore show that ATG7 has roles in invasion and metastasis that are not related to the role of the protein in the regulation of autophagy.

Grid inhomogeneous solvation theory for cross-solvation in rigid solvents.

Grid Inhomogeneous Solvation Theory (GIST) has proven useful to calculate localized thermodynamic properties of water around a solute. Numerous studies have leveraged this information to enhance structure-based binding predictions. We have recently extended GIST toward chloroform as a solvent to allow the prediction of passive membrane permeability. Here, we further generalize the GIST algorithm toward all solvents that can be modeled as rigid molecules. This restriction is inherent to the method and is already present in the inhomogeneous solvation theory. Here, we show that our approach can be applied to various solvent molecules by comparing the results of GIST simulations with thermodynamic integration (TI) calculations and experimental results. Additionally, we analyze and compare a matrix consisting of 100 entries of ten different solvent molecules solvated within each other. We find that the GIST results are highly correlated with TI calculations as well as experiments. For some solvents, we find Pearson correlations of up to 0.99 to the true entropy, while others are affected by the first-order approximation more strongly. The enthalpy-entropy splitting provided by GIST allows us to extend a recently published approach, which estimates higher order entropies by a linear scaling of the first-order entropy, to solvents other than water. Furthermore, we investigate the convergence of GIST in different solvents. We conclude that our extension to GIST reliably calculates localized thermodynamic properties for different solvents and thereby significantly extends the applicability of this widely used method.

Corrigendum: Comparing Antibody Interfaces to Inform Rational Design of New Antibody Formats.

[This corrects the article DOI: 10.3389/fmolb.2022.812750.].

Efficient few-cycle Yb-doped laser oscillator with Watt-level average power.

So far, the operation of ultrafast bulk laser oscillators based on Yb-doped gain materials and directly emitting few-cycle pulses have been restricted to low optical-to-optical efficiencies and average output powers of only a few milliwatt. This performance limitation can be attributed to the commonly-applied standard collinear pumping scheme in which the optical pump is transmitted through a dichroic mirror whose spectral transmission and dispersion properties severely perturb the oscillating pulse when its optical spectrum extends towards the pump wavelength. In this study, we report on a novel pumping scheme relying on cross polarization that overcomes this challenge. In our concept, the pump transmitting mirror is highly transmissive for the pump light in p-polarization, while it is highly reflective for the laser light in s-polarization over a broad wavelength range, even covering the pump wavelength and beyond. In contrast to a standard thin-film polarizer featuring similar polarization dependent properties, it provides a low and flat dispersion profile over a broad spectral range for the s-polarization. Implementing this pumping scheme in a soft-aperture Kerr-lens mode-locked bulk laser oscillator based on the gain material Yb:CALGO, we achieve clean 22-fs soliton pulses at 729 mW of average output power and an optical-to-optical efficiency of 25%. In a second configuration optimized for the highest average output power, we demonstrate a high optical-to-optical efficiency of 36.6%, which was obtained for 31-fs pulses at 1.63 W of average output power. In a third configuration we experimentally confirm the limiting effect of a dichroic mirror commonly used in the standard collinear pumping scheme. All the results presented here and obtained in the first and second configuration generate pulses with a center wavelength ranging from 1030 nm to 1056 nm, well within the spectral region of high gain cross sections of Yb:CALGO. While this initial demonstration was realized using a commercial diffraction-limited fiber laser as pump source, the pump geometry appears also well suited for pumping with laser diodes coupled into multimode fibers. This novel approach opens up new opportunities for compact and cost-efficient high-power few-cycle bulk laser oscillators based on Yb-doped gain materials and can be applied to any gain material with small quantum defect.